Starting phenix.real_space_refine on Mon Jan 13 19:37:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y3v_38900/01_2025/8y3v_38900.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y3v_38900/01_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_38900/01_2025/8y3v_38900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y3v_38900/01_2025/8y3v_38900.map" model { file = "/net/cci-nas-00/data/ceres_data/8y3v_38900/01_2025/8y3v_38900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y3v_38900/01_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-5571/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: 3.07, per 1000 atoms: 0.81 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: 0.80 Conformation dependent library (CDL) restraints added in 450.8 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: 0.48 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: 0.96 Time building geometry restraints manager: 0.94 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.230 Find NCS groups from input model: 0.160 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.340 ------------------------------------------------------------------------------- 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= 0.386 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 *********************** 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 : 0.429 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: 0.1334 time to fit residues: 9.8082 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 : 0.426 ------------------------------------------------------------------------------- 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: 0.0050 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: 1.4000 ------------------------------------------------------------------------------- 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 = 0.119704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.092771 restraints weight = 4766.958| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.72 r_work: 0.2940 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.0956 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= 0.190 Angle : 0.577 5.661 5259 Z= 0.309 Chirality : 0.047 0.134 633 Planarity : 0.005 0.041 679 Dihedral : 5.077 22.420 537 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.49 % Allowed : 8.98 % Favored : 90.53 % 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: -1.44 (0.38), residues: 505 helix: 0.98 (0.50), residues: 100 sheet: -0.89 (0.37), residues: 200 loop : -1.93 (0.43), residues: 205 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 A 58 ARG 0.002 0.000 ARG C 49 *********************** 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 55 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.400 Fit side-chains REVERT: B 103 LEU cc_start: 0.8337 (tp) cc_final: 0.8103 (tp) outliers start: 2 outliers final: 0 residues processed: 54 average time/residue: 0.1280 time to fit residues: 9.1887 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 : 0.427 ------------------------------------------------------------------------------- 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: 2.9990 chunk 21 optimal weight: 8.9990 chunk 22 optimal weight: 0.7980 chunk 15 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 = 0.3385 r_free = 0.3385 target = 0.118566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.091753 restraints weight = 4786.645| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.71 r_work: 0.2876 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1118 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= 0.248 Angle : 0.580 5.707 5259 Z= 0.308 Chirality : 0.047 0.131 633 Planarity : 0.005 0.039 679 Dihedral : 4.941 22.157 537 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 0.73 % Allowed : 14.56 % Favored : 84.71 % 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: -1.21 (0.38), residues: 505 helix: 1.36 (0.52), residues: 100 sheet: -0.59 (0.37), residues: 207 loop : -2.15 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 32 PHE 0.017 0.002 PHE D 25 TYR 0.009 0.001 TYR A 58 ARG 0.001 0.000 ARG A 83 *********************** 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 56 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.395 Fit side-chains REVERT: B 103 LEU cc_start: 0.8328 (tp) cc_final: 0.8098 (tp) REVERT: D 102 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7503 (mp0) outliers start: 3 outliers final: 1 residues processed: 55 average time/residue: 0.1097 time to fit residues: 8.2526 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 : 0.406 ------------------------------------------------------------------------------- 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: 8.9990 chunk 31 optimal weight: 8.9990 chunk 13 optimal weight: 0.4980 chunk 33 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 37 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 overall best weight: 2.0382 ------------------------------------------------------------------------------- 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 = 0.3385 r_free = 0.3385 target = 0.118733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.091729 restraints weight = 4776.237| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.72 r_work: 0.2867 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1269 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= 0.230 Angle : 0.568 5.676 5259 Z= 0.302 Chirality : 0.047 0.130 633 Planarity : 0.004 0.036 679 Dihedral : 4.865 21.590 537 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 1.21 % Allowed : 15.05 % Favored : 83.74 % 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: -1.08 (0.38), residues: 505 helix: 1.55 (0.52), residues: 100 sheet: -0.47 (0.37), residues: 206 loop : -2.17 (0.41), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 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 A 83 *********************** 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: 5 poor density : 53 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: B 103 LEU cc_start: 0.8325 (tp) cc_final: 0.8096 (tp) outliers start: 5 outliers final: 4 residues processed: 57 average time/residue: 0.1132 time to fit residues: 8.8792 Evaluate side-chains 54 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 69 THR 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: 10.0000 chunk 40 optimal weight: 8.9990 chunk 47 optimal weight: 0.3980 chunk 21 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 overall best weight: 2.0584 ------------------------------------------------------------------------------- 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 = 0.3384 r_free = 0.3384 target = 0.118626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.091453 restraints weight = 4901.767| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.76 r_work: 0.2886 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1335 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= 0.231 Angle : 0.567 5.673 5259 Z= 0.300 Chirality : 0.047 0.131 633 Planarity : 0.004 0.034 679 Dihedral : 4.819 21.553 537 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 2.43 % Allowed : 16.99 % Favored : 80.58 % 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: -0.95 (0.38), residues: 505 helix: 1.68 (0.51), residues: 100 sheet: -0.34 (0.37), residues: 207 loop : -2.16 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 32 PHE 0.012 0.002 PHE D 25 TYR 0.009 0.001 TYR D 58 ARG 0.001 0.000 ARG A 83 *********************** 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: 10 poor density : 50 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: B 103 LEU cc_start: 0.8347 (tp) cc_final: 0.8119 (tp) outliers start: 10 outliers final: 5 residues processed: 59 average time/residue: 0.1065 time to fit residues: 8.6518 Evaluate side-chains 55 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 69 THR 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: 0.5980 chunk 3 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 39 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 43 optimal weight: 0.1980 chunk 29 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3411 r_free = 0.3411 target = 0.120335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.093378 restraints weight = 4767.532| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.73 r_work: 0.2967 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1559 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= 0.159 Angle : 0.533 5.598 5259 Z= 0.281 Chirality : 0.046 0.129 633 Planarity : 0.004 0.033 679 Dihedral : 4.554 20.512 537 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.43 % Allowed : 16.75 % 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 (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: -0.78 (0.38), residues: 505 helix: 1.92 (0.51), residues: 100 sheet: -0.24 (0.36), residues: 212 loop : -2.17 (0.41), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 32 PHE 0.009 0.001 PHE D 25 TYR 0.010 0.001 TYR D 58 ARG 0.001 0.000 ARG A 83 *********************** 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 70 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: B 113 LYS cc_start: 0.8611 (ttmt) cc_final: 0.7953 (tttm) outliers start: 10 outliers final: 6 residues processed: 69 average time/residue: 0.1118 time to fit residues: 10.4812 Evaluate side-chains 61 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 69 THR 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: 8.9990 chunk 1 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 0.1980 chunk 27 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.3407 r_free = 0.3407 target = 0.120316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.093164 restraints weight = 4771.522| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.74 r_work: 0.2941 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3851 Z= 0.184 Angle : 0.546 5.629 5259 Z= 0.287 Chirality : 0.046 0.129 633 Planarity : 0.004 0.032 679 Dihedral : 4.523 20.210 537 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 1.70 % Allowed : 18.93 % 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: -0.58 (0.38), residues: 505 helix: 2.08 (0.50), residues: 100 sheet: -0.07 (0.37), residues: 214 loop : -2.13 (0.41), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 32 PHE 0.009 0.001 PHE D 25 TYR 0.014 0.001 TYR A 58 ARG 0.001 0.000 ARG A 49 *********************** 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: 7 poor density : 56 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: B 113 LYS cc_start: 0.8660 (ttmt) cc_final: 0.8020 (tttm) outliers start: 7 outliers final: 6 residues processed: 62 average time/residue: 0.1147 time to fit residues: 9.6085 Evaluate side-chains 60 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 69 THR 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: 2.9990 chunk 47 optimal weight: 0.5980 chunk 18 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 = 0.3390 r_free = 0.3390 target = 0.119278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.092137 restraints weight = 4792.491| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.74 r_work: 0.2909 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1638 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= 0.222 Angle : 0.566 5.654 5259 Z= 0.299 Chirality : 0.047 0.151 633 Planarity : 0.004 0.033 679 Dihedral : 4.644 20.458 537 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.21 % Allowed : 19.90 % Favored : 78.88 % 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: 2.06 (0.50), residues: 100 sheet: -0.06 (0.36), residues: 214 loop : -2.13 (0.41), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 32 PHE 0.010 0.001 PHE D 25 TYR 0.012 0.001 TYR A 58 ARG 0.001 0.000 ARG A 49 *********************** 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 57 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: B 113 LYS cc_start: 0.8654 (ttmt) cc_final: 0.8014 (tttm) outliers start: 5 outliers final: 5 residues processed: 57 average time/residue: 0.1142 time to fit residues: 8.8260 Evaluate side-chains 55 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.3337 r_free = 0.3337 target = 0.115473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.088615 restraints weight = 4862.590| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.70 r_work: 0.2878 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 3851 Z= 0.470 Angle : 0.693 5.812 5259 Z= 0.367 Chirality : 0.051 0.147 633 Planarity : 0.005 0.036 679 Dihedral : 5.275 23.856 537 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.29 % Favored : 88.71 % Rotamer: Outliers : 1.94 % Allowed : 20.39 % 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: -0.93 (0.37), residues: 505 helix: 1.73 (0.50), residues: 99 sheet: -0.41 (0.37), residues: 207 loop : -2.07 (0.41), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 32 PHE 0.012 0.002 PHE D 25 TYR 0.010 0.002 TYR A 42 ARG 0.001 0.000 ARG D 49 *********************** 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 61 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.405 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 59 average time/residue: 0.1267 time to fit residues: 10.0522 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 : 0.429 ------------------------------------------------------------------------------- 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 47 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.3384 r_free = 0.3384 target = 0.118711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.091455 restraints weight = 4821.744| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.73 r_work: 0.2942 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1640 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= 0.217 Angle : 0.591 5.676 5259 Z= 0.310 Chirality : 0.048 0.137 633 Planarity : 0.004 0.036 679 Dihedral : 4.898 20.514 537 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 1.94 % Allowed : 19.66 % 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 (0.37), residues: 505 helix: 1.84 (0.49), residues: 99 sheet: -0.35 (0.37), residues: 206 loop : -2.01 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 32 PHE 0.010 0.001 PHE D 25 TYR 0.012 0.001 TYR A 58 ARG 0.001 0.000 ARG B 49 ********************** 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 60 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.394 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 59 average time/residue: 0.1068 time to fit residues: 8.7265 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 : 0.430 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 36 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.3396 r_free = 0.3396 target = 0.119593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.092999 restraints weight = 4722.344| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.65 r_work: 0.2879 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3851 Z= 0.212 Angle : 0.587 5.705 5259 Z= 0.306 Chirality : 0.047 0.134 633 Planarity : 0.004 0.035 679 Dihedral : 4.775 20.304 537 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 1.70 % Allowed : 19.66 % Favored : 78.64 % 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 (0.37), residues: 505 helix: 2.04 (0.50), residues: 99 sheet: -0.29 (0.37), residues: 206 loop : -1.99 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 32 PHE 0.009 0.001 PHE D 25 TYR 0.011 0.001 TYR A 58 ARG 0.001 0.000 ARG A 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2030.14 seconds wall clock time: 36 minutes 55.87 seconds (2215.87 seconds total)