Starting phenix.real_space_refine on Fri Dec 27 09:04:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y3v_38900/12_2024/8y3v_38900.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y3v_38900/12_2024/8y3v_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_38900/12_2024/8y3v_38900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y3v_38900/12_2024/8y3v_38900.map" model { file = "/net/cci-nas-00/data/ceres_data/8y3v_38900/12_2024/8y3v_38900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y3v_38900/12_2024/8y3v_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-5532/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: 3.38, per 1000 atoms: 0.89 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: 0.95 Conformation dependent library (CDL) restraints added in 566.9 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: 0.50 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: 0.99 Time building geometry restraints manager: 1.10 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: 0.770 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.260 Find NCS groups from input model: 0.170 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.350 ------------------------------------------------------------------------------- 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 : 0.435 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: 0.1241 time to fit residues: 9.1061 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 : 0.458 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 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 : 0.437 Fit side-chains REVERT: B 103 LEU cc_start: 0.8429 (tp) cc_final: 0.8208 (tp) outliers start: 2 outliers final: 0 residues processed: 54 average time/residue: 0.1274 time to fit residues: 9.2247 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 : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3851 Z= 0.185 Angle : 0.548 5.650 5259 Z= 0.290 Chirality : 0.047 0.133 633 Planarity : 0.005 0.038 679 Dihedral : 4.776 21.665 537 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 0.73 % Allowed : 13.59 % Favored : 85.68 % 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: -1.12 (0.38), residues: 505 helix: 1.48 (0.52), residues: 100 sheet: -0.54 (0.37), residues: 206 loop : -2.10 (0.41), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 32 PHE 0.015 0.002 PHE D 25 TYR 0.010 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 58 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.718 Fit side-chains REVERT: B 103 LEU cc_start: 0.8436 (tp) cc_final: 0.8231 (tp) outliers start: 3 outliers final: 1 residues processed: 57 average time/residue: 0.1205 time to fit residues: 9.5744 Evaluate side-chains 53 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 26 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3851 Z= 0.341 Angle : 0.619 5.790 5259 Z= 0.329 Chirality : 0.048 0.132 633 Planarity : 0.005 0.038 679 Dihedral : 5.027 22.168 537 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 1.46 % Allowed : 16.02 % Favored : 82.52 % 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: -1.18 (0.38), residues: 505 helix: 1.41 (0.51), residues: 100 sheet: -0.62 (0.38), residues: 200 loop : -2.05 (0.41), 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 D 58 ARG 0.001 0.000 ARG D 49 *********************** 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 57 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.362 Fit side-chains REVERT: B 103 LEU cc_start: 0.8461 (tp) cc_final: 0.8242 (tp) outliers start: 6 outliers final: 3 residues processed: 54 average time/residue: 0.1112 time to fit residues: 8.1813 Evaluate side-chains 52 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 69 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 39 optimal weight: 0.0000 chunk 32 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1360 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= 0.243 Angle : 0.573 5.691 5259 Z= 0.304 Chirality : 0.047 0.131 633 Planarity : 0.004 0.035 679 Dihedral : 4.853 21.175 537 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 2.18 % Allowed : 16.50 % Favored : 81.31 % 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: 1.64 (0.51), residues: 100 sheet: -0.44 (0.38), residues: 200 loop : -2.03 (0.40), residues: 205 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 0.009 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 63 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.462 Fit side-chains REVERT: B 103 LEU cc_start: 0.8433 (tp) cc_final: 0.8220 (tp) REVERT: B 113 LYS cc_start: 0.8563 (ttmt) cc_final: 0.8016 (tttm) outliers start: 9 outliers final: 5 residues processed: 61 average time/residue: 0.1093 time to fit residues: 9.0682 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 : 0.468 ------------------------------------------------------------------------------- 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 69 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 38 optimal weight: 0.0170 chunk 21 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 overall best weight: 1.6026 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1546 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= 0.197 Angle : 0.559 5.644 5259 Z= 0.294 Chirality : 0.046 0.130 633 Planarity : 0.004 0.033 679 Dihedral : 4.709 21.199 537 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.43 % Allowed : 17.48 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.85 (0.51), residues: 100 sheet: -0.24 (0.36), residues: 214 loop : -2.14 (0.41), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 32 PHE 0.010 0.001 PHE D 25 TYR 0.009 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 64 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.436 Fit side-chains REVERT: B 103 LEU cc_start: 0.8457 (tp) cc_final: 0.8252 (tp) REVERT: B 113 LYS cc_start: 0.8552 (ttmt) cc_final: 0.7998 (tttm) REVERT: D 71 THR cc_start: 0.8494 (OUTLIER) cc_final: 0.8141 (p) outliers start: 10 outliers final: 6 residues processed: 61 average time/residue: 0.1088 time to fit residues: 9.0477 Evaluate side-chains 59 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 72 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 4.9990 chunk 39 optimal weight: 0.0770 chunk 25 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 21 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1605 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= 0.196 Angle : 0.552 5.642 5259 Z= 0.291 Chirality : 0.046 0.131 633 Planarity : 0.004 0.033 679 Dihedral : 4.607 20.328 537 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 1.70 % Allowed : 18.20 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.70 (0.38), residues: 505 helix: 1.99 (0.50), residues: 100 sheet: -0.17 (0.36), residues: 214 loop : -2.17 (0.41), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 32 PHE 0.010 0.001 PHE D 25 TYR 0.009 0.001 TYR D 58 ARG 0.001 0.000 ARG A 83 *********************** 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 68 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.441 Fit side-chains REVERT: B 113 LYS cc_start: 0.8532 (ttmt) cc_final: 0.7982 (tttm) REVERT: D 71 THR cc_start: 0.8514 (OUTLIER) cc_final: 0.8169 (p) outliers start: 7 outliers final: 6 residues processed: 66 average time/residue: 0.1012 time to fit residues: 9.2384 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 : 0.408 ------------------------------------------------------------------------------- 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 C residue 108 MET Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 72 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 42 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3851 Z= 0.293 Angle : 0.607 5.715 5259 Z= 0.320 Chirality : 0.048 0.157 633 Planarity : 0.004 0.034 679 Dihedral : 4.856 21.509 537 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % 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: -0.76 (0.37), residues: 505 helix: 1.98 (0.50), residues: 100 sheet: -0.32 (0.37), residues: 207 loop : -2.03 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 32 PHE 0.011 0.002 PHE D 25 TYR 0.013 0.001 TYR A 58 ARG 0.001 0.000 ARG D 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 60 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.436 Fit side-chains REVERT: B 40 GLN cc_start: 0.8942 (tp-100) cc_final: 0.8661 (tp-100) REVERT: B 113 LYS cc_start: 0.8535 (ttmt) cc_final: 0.7984 (tttm) REVERT: D 71 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8396 (m) outliers start: 8 outliers final: 6 residues processed: 58 average time/residue: 0.1065 time to fit residues: 8.5996 Evaluate side-chains 58 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 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 8 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 72 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 47 optimal weight: 0.3980 overall best weight: 3.0788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3851 Z= 0.323 Angle : 0.625 5.735 5259 Z= 0.330 Chirality : 0.049 0.142 633 Planarity : 0.004 0.038 679 Dihedral : 5.054 22.672 537 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % 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: -0.85 (0.37), residues: 505 helix: 1.92 (0.49), residues: 99 sheet: -0.38 (0.36), residues: 207 loop : -2.06 (0.41), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 32 PHE 0.012 0.002 PHE D 25 TYR 0.012 0.001 TYR A 58 ARG 0.001 0.000 ARG A 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 : 0.436 Fit side-chains REVERT: D 71 THR cc_start: 0.8653 (OUTLIER) cc_final: 0.8414 (m) outliers start: 8 outliers final: 6 residues processed: 59 average time/residue: 0.1185 time to fit residues: 9.4435 Evaluate side-chains 57 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 C residue 108 MET Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 72 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 4.9990 chunk 38 optimal weight: 0.0000 chunk 3 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1768 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= 0.172 Angle : 0.568 5.641 5259 Z= 0.296 Chirality : 0.047 0.136 633 Planarity : 0.004 0.033 679 Dihedral : 4.710 19.712 537 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 1.94 % Allowed : 19.90 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.67 (0.37), residues: 505 helix: 2.16 (0.49), residues: 100 sheet: -0.19 (0.36), residues: 212 loop : -2.16 (0.41), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 32 PHE 0.008 0.001 PHE D 25 TYR 0.013 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 63 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.448 Fit side-chains REVERT: B 113 LYS cc_start: 0.8517 (ttmt) cc_final: 0.7954 (tttm) REVERT: D 71 THR cc_start: 0.8649 (OUTLIER) cc_final: 0.8440 (m) outliers start: 8 outliers final: 5 residues processed: 61 average time/residue: 0.1164 time to fit residues: 9.8838 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 : 0.415 ------------------------------------------------------------------------------- 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 71 THR Chi-restraints excluded: chain D residue 72 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 0.3980 chunk 15 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.118524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.091920 restraints weight = 4785.838| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.67 r_work: 0.2917 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1644 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= 0.271 Angle : 0.605 5.684 5259 Z= 0.317 Chirality : 0.048 0.133 633 Planarity : 0.004 0.035 679 Dihedral : 4.839 20.529 537 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 1.46 % Allowed : 19.90 % 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: -0.71 (0.37), residues: 505 helix: 2.24 (0.49), residues: 99 sheet: -0.31 (0.37), residues: 207 loop : -2.07 (0.41), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 32 PHE 0.009 0.002 PHE D 25 TYR 0.012 0.001 TYR A 58 ARG 0.001 0.000 ARG D 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1149.37 seconds wall clock time: 21 minutes 37.05 seconds (1297.05 seconds total)