Starting phenix.real_space_refine on Thu Dec 7 22:10:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t05_40935/12_2023/8t05_40935_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t05_40935/12_2023/8t05_40935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t05_40935/12_2023/8t05_40935.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t05_40935/12_2023/8t05_40935.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t05_40935/12_2023/8t05_40935_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t05_40935/12_2023/8t05_40935_updated.pdb" } resolution = 3.22 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= 0.004 sd= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2 5.49 5 S 22 5.16 5 C 3387 2.51 5 N 798 2.21 5 O 893 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 202": "OD1" <-> "OD2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 137": "OE1" <-> "OE2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "B ASP 202": "OD1" <-> "OD2" Residue "C GLU 10": "OE1" <-> "OE2" Residue "C TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 105": "NH1" <-> "NH2" Residue "D ARG 24": "NH1" <-> "NH2" Residue "D ASP 56": "OD1" <-> "OD2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 5104 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1592 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 7, 'TRANS': 193} Chain: "B" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1592 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 7, 'TRANS': 193} Chain: "C" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "D" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 72 Unusual residues: {' ZN': 1, 'CLR': 1, 'LBN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 72 Unusual residues: {' ZN': 1, 'CLR': 1, 'LBN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 3.20, per 1000 atoms: 0.63 Number of scatterers: 5104 At special positions: 0 Unit cell: (81.34, 88.81, 113.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 22 16.00 P 2 15.00 O 893 8.00 N 798 7.00 C 3387 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 60 " distance=2.04 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 60 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 1.83 Conformation dependent library (CDL) restraints added in 878.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 182 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 186 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 48 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 48 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 186 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 182 " 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1158 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 20 helices and 4 sheets defined 50.9% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 3 through 27 Proline residue: A 11 - end of helix removed outlier: 3.973A pdb=" N GLY A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA A 17 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N PHE A 18 " --> pdb=" O SER A 14 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N PHE A 19 " --> pdb=" O SER A 15 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE A 20 " --> pdb=" O GLY A 16 " (cutoff:3.500A) Proline residue: A 21 - end of helix Processing helix chain 'A' and resid 31 through 50 removed outlier: 4.083A pdb=" N LEU A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 62 removed outlier: 3.692A pdb=" N MET A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 85 removed outlier: 3.738A pdb=" N THR A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 111 Processing helix chain 'A' and resid 120 through 141 Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 155 through 170 Processing helix chain 'A' and resid 178 through 199 removed outlier: 3.787A pdb=" N SER A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG A 198 " --> pdb=" O THR A 194 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 27 Proline residue: B 11 - end of helix removed outlier: 3.986A pdb=" N GLY B 16 " --> pdb=" O ALA B 12 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA B 17 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N PHE B 18 " --> pdb=" O SER B 14 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N PHE B 19 " --> pdb=" O SER B 15 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE B 20 " --> pdb=" O GLY B 16 " (cutoff:3.500A) Proline residue: B 21 - end of helix Processing helix chain 'B' and resid 31 through 51 Processing helix chain 'B' and resid 56 through 58 No H-bonds generated for 'chain 'B' and resid 56 through 58' Processing helix chain 'B' and resid 64 through 85 removed outlier: 3.628A pdb=" N PHE B 69 " --> pdb=" O LYS B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 111 Processing helix chain 'B' and resid 120 through 140 Processing helix chain 'B' and resid 148 through 152 Processing helix chain 'B' and resid 155 through 170 Processing helix chain 'B' and resid 178 through 198 removed outlier: 3.965A pdb=" N SER B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG B 198 " --> pdb=" O THR B 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'C' and resid 17 through 23 Processing sheet with id= B, first strand: chain 'C' and resid 116 through 118 removed outlier: 3.622A pdb=" N ALA C 92 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LYS C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N TRP C 47 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR C 40 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LEU C 45 " --> pdb=" O THR C 40 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.560A pdb=" N LYS D 103 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL D 13 " --> pdb=" O LYS D 103 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N GLU D 105 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 19 through 24 removed outlier: 3.533A pdb=" N VAL D 19 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) 262 hydrogen bonds defined for protein. 771 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: 1.27 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 746 1.31 - 1.44: 1499 1.44 - 1.56: 2946 1.56 - 1.69: 14 1.69 - 1.82: 32 Bond restraints: 5237 Sorted by residual: bond pdb=" C GLY C 8 " pdb=" N ALA C 9 " ideal model delta sigma weight residual 1.331 1.409 -0.077 1.30e-02 5.92e+03 3.53e+01 bond pdb=" C25 LBN A 303 " pdb=" O5 LBN A 303 " ideal model delta sigma weight residual 1.326 1.433 -0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" C25 LBN B 303 " pdb=" O5 LBN B 303 " ideal model delta sigma weight residual 1.326 1.429 -0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" C34 LBN A 303 " pdb=" O7 LBN A 303 " ideal model delta sigma weight residual 1.331 1.427 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C34 LBN B 303 " pdb=" O7 LBN B 303 " ideal model delta sigma weight residual 1.331 1.424 -0.093 2.00e-02 2.50e+03 2.16e+01 ... (remaining 5232 not shown) Histogram of bond angle deviations from ideal: 99.17 - 106.22: 126 106.22 - 113.28: 2774 113.28 - 120.34: 2328 120.34 - 127.40: 1834 127.40 - 134.45: 43 Bond angle restraints: 7105 Sorted by residual: angle pdb=" N PHE C 109 " pdb=" CA PHE C 109 " pdb=" C PHE C 109 " ideal model delta sigma weight residual 111.24 118.85 -7.61 1.38e+00 5.25e-01 3.04e+01 angle pdb=" C GLY A 101 " pdb=" N GLY A 102 " pdb=" CA GLY A 102 " ideal model delta sigma weight residual 120.03 125.59 -5.56 1.12e+00 7.97e-01 2.47e+01 angle pdb=" N THR D 94 " pdb=" CA THR D 94 " pdb=" C THR D 94 " ideal model delta sigma weight residual 108.82 117.00 -8.18 1.65e+00 3.67e-01 2.46e+01 angle pdb=" O1 LBN B 303 " pdb=" P1 LBN B 303 " pdb=" O2 LBN B 303 " ideal model delta sigma weight residual 93.45 108.05 -14.60 3.00e+00 1.11e-01 2.37e+01 angle pdb=" O1 LBN A 303 " pdb=" P1 LBN A 303 " pdb=" O2 LBN A 303 " ideal model delta sigma weight residual 93.45 107.88 -14.43 3.00e+00 1.11e-01 2.31e+01 ... (remaining 7100 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.48: 3038 30.48 - 60.96: 92 60.96 - 91.44: 11 91.44 - 121.92: 7 121.92 - 152.40: 4 Dihedral angle restraints: 3152 sinusoidal: 1337 harmonic: 1815 Sorted by residual: dihedral pdb=" CA THR D 94 " pdb=" C THR D 94 " pdb=" N PRO D 95 " pdb=" CA PRO D 95 " ideal model delta harmonic sigma weight residual 180.00 70.79 109.21 0 5.00e+00 4.00e-02 4.77e+02 dihedral pdb=" CA ALA D 50 " pdb=" C ALA D 50 " pdb=" N ALA D 51 " pdb=" CA ALA D 51 " ideal model delta harmonic sigma weight residual -180.00 -151.52 -28.48 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA SER B 56 " pdb=" C SER B 56 " pdb=" N LEU B 57 " pdb=" CA LEU B 57 " ideal model delta harmonic sigma weight residual -180.00 -155.12 -24.88 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 3149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.985: 803 0.985 - 1.969: 0 1.969 - 2.954: 0 2.954 - 3.938: 0 3.938 - 4.923: 2 Chirality restraints: 805 Sorted by residual: chirality pdb=" C2 LBN B 303 " pdb=" C1 LBN B 303 " pdb=" C3 LBN B 303 " pdb=" O7 LBN B 303 " both_signs ideal model delta sigma weight residual False -2.36 2.56 -4.92 2.00e-01 2.50e+01 6.06e+02 chirality pdb=" C2 LBN A 303 " pdb=" C1 LBN A 303 " pdb=" C3 LBN A 303 " pdb=" O7 LBN A 303 " both_signs ideal model delta sigma weight residual False -2.36 2.55 -4.92 2.00e-01 2.50e+01 6.04e+02 chirality pdb=" C14 CLR A 302 " pdb=" C13 CLR A 302 " pdb=" C15 CLR A 302 " pdb=" C8 CLR A 302 " both_signs ideal model delta sigma weight residual False -2.32 -2.72 0.40 2.00e-01 2.50e+01 3.97e+00 ... (remaining 802 not shown) Planarity restraints: 848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 145 " -0.060 5.00e-02 4.00e+02 9.05e-02 1.31e+01 pdb=" N PRO B 146 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO B 146 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 146 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 13 " -0.054 5.00e-02 4.00e+02 8.29e-02 1.10e+01 pdb=" N PRO C 14 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO C 14 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 14 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 94 " -0.042 5.00e-02 4.00e+02 6.45e-02 6.65e+00 pdb=" N PRO D 95 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 95 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 95 " -0.036 5.00e-02 4.00e+02 ... (remaining 845 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 71 2.68 - 3.23: 4644 3.23 - 3.79: 7743 3.79 - 4.34: 10751 4.34 - 4.90: 18020 Nonbonded interactions: 41229 Sorted by model distance: nonbonded pdb=" OE1 GLN A 44 " pdb="ZN ZN A 301 " model vdw 2.120 2.230 nonbonded pdb=" OE1 GLN B 44 " pdb="ZN ZN B 301 " model vdw 2.172 2.230 nonbonded pdb=" NH2 ARG D 61 " pdb=" OE2 GLU D 81 " model vdw 2.356 2.520 nonbonded pdb=" NH2 ARG A 108 " pdb=" O PRO A 116 " model vdw 2.413 2.520 nonbonded pdb=" O HIS D 90 " pdb=" ND1 HIS D 90 " model vdw 2.433 2.520 ... (remaining 41224 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.010 Normalize map: mean=0, sd=1: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.730 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 18.400 Find NCS groups from input model: 0.200 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 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 : 0.014 0.107 5237 Z= 0.934 Angle : 1.851 14.605 7105 Z= 1.350 Chirality : 0.259 4.923 805 Planarity : 0.006 0.091 848 Dihedral : 16.958 152.400 1982 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.78 % Favored : 93.90 % Rotamer: Outliers : 0.93 % Allowed : 6.16 % Favored : 92.91 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: -2.10 (0.31), residues: 623 helix: -1.21 (0.25), residues: 313 sheet: -1.44 (0.49), residues: 86 loop : -1.32 (0.44), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 151 HIS 0.007 0.002 HIS D 90 PHE 0.019 0.002 PHE B 43 TYR 0.043 0.003 TYR D 49 ARG 0.003 0.000 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 0.537 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 92 average time/residue: 0.2246 time to fit residues: 25.4630 Evaluate side-chains 78 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.568 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.0503 time to fit residues: 1.0850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.0870 chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 95 HIS D 6 GLN ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5237 Z= 0.191 Angle : 0.623 7.846 7105 Z= 0.320 Chirality : 0.041 0.180 805 Planarity : 0.005 0.076 848 Dihedral : 16.339 147.760 881 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.49 % Allowed : 10.63 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 0.27 (0.34), residues: 623 helix: 1.26 (0.28), residues: 314 sheet: -0.79 (0.49), residues: 110 loop : -0.88 (0.48), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 47 HIS 0.004 0.001 HIS C 35 PHE 0.016 0.002 PHE A 39 TYR 0.014 0.001 TYR D 49 ARG 0.002 0.000 ARG A 140 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.509 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 84 average time/residue: 0.2070 time to fit residues: 21.8800 Evaluate side-chains 79 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 0.559 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0529 time to fit residues: 1.1884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 19 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 HIS B 113 ASN B 186 HIS ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5237 Z= 0.212 Angle : 0.583 6.150 7105 Z= 0.295 Chirality : 0.041 0.198 805 Planarity : 0.005 0.078 848 Dihedral : 14.517 143.892 881 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.49 % Allowed : 11.57 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 0.88 (0.35), residues: 623 helix: 2.02 (0.29), residues: 307 sheet: -0.59 (0.51), residues: 107 loop : -0.94 (0.47), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 47 HIS 0.005 0.001 HIS C 35 PHE 0.014 0.001 PHE B 70 TYR 0.015 0.001 TYR D 49 ARG 0.003 0.000 ARG B 198 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 78 time to evaluate : 0.527 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 82 average time/residue: 0.2054 time to fit residues: 21.2665 Evaluate side-chains 81 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 75 time to evaluate : 0.548 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0584 time to fit residues: 1.3489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5237 Z= 0.243 Angle : 0.593 7.062 7105 Z= 0.300 Chirality : 0.041 0.195 805 Planarity : 0.005 0.080 848 Dihedral : 13.383 153.144 881 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.93 % Allowed : 13.06 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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 (0.35), residues: 623 helix: 2.10 (0.29), residues: 307 sheet: -0.36 (0.50), residues: 105 loop : -1.10 (0.46), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 112 HIS 0.005 0.001 HIS C 35 PHE 0.016 0.002 PHE D 91 TYR 0.017 0.001 TYR D 49 ARG 0.005 0.000 ARG B 198 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 0.560 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 77 average time/residue: 0.2051 time to fit residues: 19.9922 Evaluate side-chains 78 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.522 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0532 time to fit residues: 1.1223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 15 optimal weight: 0.0040 chunk 20 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5237 Z= 0.199 Angle : 0.545 6.066 7105 Z= 0.276 Chirality : 0.040 0.196 805 Planarity : 0.005 0.079 848 Dihedral : 12.341 153.005 881 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.75 % Allowed : 13.99 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 1.02 (0.35), residues: 623 helix: 2.28 (0.29), residues: 308 sheet: -0.42 (0.50), residues: 105 loop : -1.19 (0.46), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 47 HIS 0.004 0.001 HIS C 35 PHE 0.014 0.001 PHE B 70 TYR 0.014 0.001 TYR D 49 ARG 0.004 0.000 ARG B 198 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 0.521 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 73 average time/residue: 0.2190 time to fit residues: 20.1906 Evaluate side-chains 72 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 70 time to evaluate : 0.573 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0772 time to fit residues: 1.0249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5237 Z= 0.227 Angle : 0.561 6.099 7105 Z= 0.284 Chirality : 0.040 0.198 805 Planarity : 0.005 0.079 848 Dihedral : 12.077 160.657 881 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.37 % Allowed : 15.11 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 1.03 (0.35), residues: 623 helix: 2.19 (0.28), residues: 318 sheet: -0.39 (0.50), residues: 105 loop : -1.22 (0.48), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 47 HIS 0.005 0.001 HIS C 35 PHE 0.016 0.001 PHE D 91 TYR 0.016 0.001 TYR D 49 ARG 0.004 0.000 ARG B 198 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 0.552 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 71 average time/residue: 0.2207 time to fit residues: 19.7050 Evaluate side-chains 71 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 0.534 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0524 time to fit residues: 0.8485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5237 Z= 0.332 Angle : 0.630 6.804 7105 Z= 0.320 Chirality : 0.043 0.201 805 Planarity : 0.005 0.084 848 Dihedral : 12.551 177.071 881 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.56 % Allowed : 16.04 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 0.68 (0.35), residues: 623 helix: 1.86 (0.28), residues: 313 sheet: -0.61 (0.48), residues: 117 loop : -1.19 (0.49), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 47 HIS 0.007 0.002 HIS C 35 PHE 0.021 0.002 PHE D 91 TYR 0.020 0.002 TYR D 49 ARG 0.003 0.001 ARG B 198 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 0.607 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 71 average time/residue: 0.2416 time to fit residues: 21.2719 Evaluate side-chains 72 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 0.556 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0859 time to fit residues: 0.8987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 52 optimal weight: 0.0570 chunk 55 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5237 Z= 0.241 Angle : 0.571 6.212 7105 Z= 0.290 Chirality : 0.041 0.197 805 Planarity : 0.005 0.083 848 Dihedral : 11.799 177.575 881 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.37 % Allowed : 16.23 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.35), residues: 623 helix: 2.00 (0.28), residues: 318 sheet: -0.41 (0.51), residues: 108 loop : -1.35 (0.48), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 47 HIS 0.005 0.001 HIS C 35 PHE 0.015 0.001 PHE D 91 TYR 0.016 0.001 TYR D 49 ARG 0.006 0.001 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 0.590 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 72 average time/residue: 0.2142 time to fit residues: 19.2165 Evaluate side-chains 71 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 0.539 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0698 time to fit residues: 0.8548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 50 optimal weight: 0.3980 chunk 52 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 GLN ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5237 Z= 0.303 Angle : 0.610 6.681 7105 Z= 0.310 Chirality : 0.042 0.199 805 Planarity : 0.005 0.084 848 Dihedral : 11.392 169.124 881 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.19 % Allowed : 16.98 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 0.63 (0.35), residues: 623 helix: 1.86 (0.28), residues: 313 sheet: -0.71 (0.48), residues: 122 loop : -1.23 (0.50), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 47 HIS 0.006 0.002 HIS C 35 PHE 0.019 0.002 PHE D 91 TYR 0.019 0.001 TYR D 49 ARG 0.005 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 0.577 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 70 average time/residue: 0.2354 time to fit residues: 20.5988 Evaluate side-chains 69 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.620 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5237 Z= 0.201 Angle : 0.549 6.042 7105 Z= 0.278 Chirality : 0.040 0.194 805 Planarity : 0.005 0.082 848 Dihedral : 11.016 170.403 881 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 17.54 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 0.82 (0.35), residues: 623 helix: 2.14 (0.28), residues: 313 sheet: -0.37 (0.51), residues: 108 loop : -1.54 (0.46), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 47 HIS 0.004 0.001 HIS C 35 PHE 0.015 0.001 PHE A 39 TYR 0.015 0.001 TYR D 49 ARG 0.007 0.000 ARG C 13 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.570 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.2321 time to fit residues: 20.4870 Evaluate side-chains 71 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.528 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 56 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 43 GLN ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.172533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.140622 restraints weight = 5995.866| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.21 r_work: 0.3608 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5237 Z= 0.220 Angle : 0.562 6.289 7105 Z= 0.285 Chirality : 0.041 0.194 805 Planarity : 0.005 0.081 848 Dihedral : 10.881 168.832 881 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 17.91 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 0.89 (0.35), residues: 623 helix: 2.12 (0.28), residues: 318 sheet: -0.34 (0.51), residues: 108 loop : -1.44 (0.48), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 47 HIS 0.004 0.001 HIS C 35 PHE 0.015 0.001 PHE A 39 TYR 0.016 0.001 TYR D 49 ARG 0.005 0.000 ARG C 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1475.04 seconds wall clock time: 27 minutes 27.89 seconds (1647.89 seconds total)