Starting phenix.real_space_refine on Tue Feb 13 08:44:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eke_28200/02_2024/8eke_28200.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eke_28200/02_2024/8eke_28200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eke_28200/02_2024/8eke_28200.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eke_28200/02_2024/8eke_28200.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eke_28200/02_2024/8eke_28200.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eke_28200/02_2024/8eke_28200.pdb" } resolution = 3.36 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= 0.000 sd= 0.014 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 42 5.16 5 C 2966 2.51 5 N 791 2.21 5 O 882 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4681 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2343 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 291} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2338 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 291} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 3.02, per 1000 atoms: 0.65 Number of scatterers: 4681 At special positions: 0 Unit cell: (89.046, 68.967, 79.443, 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 42 16.00 O 882 8.00 N 791 7.00 C 2966 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 - 3.50 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: 1.69 Conformation dependent library (CDL) restraints added in 871.5 milliseconds 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1116 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 6 sheets defined 29.8% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 13 through 15 No H-bonds generated for 'chain 'A' and resid 13 through 15' Processing helix chain 'A' and resid 41 through 44 Processing helix chain 'A' and resid 46 through 50 removed outlier: 3.619A pdb=" N LEU A 50 " --> pdb=" O GLU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 removed outlier: 3.901A pdb=" N LEU A 57 " --> pdb=" O ASN A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 215 removed outlier: 3.621A pdb=" N VAL A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 237 removed outlier: 3.886A pdb=" N PHE A 230 " --> pdb=" O THR A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 249 Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 260 through 275 Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'B' and resid 13 through 15 No H-bonds generated for 'chain 'B' and resid 13 through 15' Processing helix chain 'B' and resid 41 through 43 No H-bonds generated for 'chain 'B' and resid 41 through 43' Processing helix chain 'B' and resid 46 through 50 removed outlier: 3.567A pdb=" N LEU B 50 " --> pdb=" O GLU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 removed outlier: 3.792A pdb=" N LEU B 57 " --> pdb=" O ASN B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 215 removed outlier: 4.127A pdb=" N VAL B 204 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 237 removed outlier: 3.921A pdb=" N PHE B 230 " --> pdb=" O THR B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 260 through 275 Processing helix chain 'B' and resid 292 through 302 Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 74 removed outlier: 8.783A pdb=" N ASN A 28 " --> pdb=" O PRO A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 103 removed outlier: 6.492A pdb=" N GLY A 149 " --> pdb=" O CYS A 160 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL A 148 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 115 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ILE A 152 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 11.412A pdb=" N THR A 111 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N PHE A 112 " --> pdb=" O GLN A 127 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLN A 127 " --> pdb=" O PHE A 112 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL A 114 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL A 125 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA A 116 " --> pdb=" O SER A 123 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103 removed outlier: 7.041A pdb=" N ALA A 173 " --> pdb=" O HIS A 164 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 73 through 74 removed outlier: 8.786A pdb=" N ASN B 28 " --> pdb=" O PRO B 39 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 101 through 103 removed outlier: 6.471A pdb=" N GLY B 149 " --> pdb=" O CYS B 160 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL B 148 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU B 115 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE B 152 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 11.426A pdb=" N THR B 111 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N PHE B 112 " --> pdb=" O GLN B 127 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLN B 127 " --> pdb=" O PHE B 112 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL B 114 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL B 125 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ALA B 116 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 101 through 103 183 hydrogen bonds defined for protein. 504 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: 1.17 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1544 1.34 - 1.46: 1084 1.46 - 1.58: 2095 1.58 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 4785 Sorted by residual: bond pdb=" C ILE A 78 " pdb=" O ILE A 78 " ideal model delta sigma weight residual 1.241 1.232 0.009 1.06e-02 8.90e+03 7.02e-01 bond pdb=" CB PRO B 99 " pdb=" CG PRO B 99 " ideal model delta sigma weight residual 1.492 1.531 -0.039 5.00e-02 4.00e+02 6.16e-01 bond pdb=" CB PRO A 99 " pdb=" CG PRO A 99 " ideal model delta sigma weight residual 1.492 1.530 -0.038 5.00e-02 4.00e+02 5.86e-01 bond pdb=" CB PRO A 52 " pdb=" CG PRO A 52 " ideal model delta sigma weight residual 1.492 1.523 -0.031 5.00e-02 4.00e+02 3.81e-01 bond pdb=" CA PRO A 184 " pdb=" C PRO A 184 " ideal model delta sigma weight residual 1.527 1.520 0.007 1.07e-02 8.73e+03 3.81e-01 ... (remaining 4780 not shown) Histogram of bond angle deviations from ideal: 100.52 - 107.22: 157 107.22 - 113.92: 2664 113.92 - 120.62: 1814 120.62 - 127.32: 1827 127.32 - 134.02: 47 Bond angle restraints: 6509 Sorted by residual: angle pdb=" N ILE B 43 " pdb=" CA ILE B 43 " pdb=" C ILE B 43 " ideal model delta sigma weight residual 113.07 108.97 4.10 1.36e+00 5.41e-01 9.10e+00 angle pdb=" C GLU A 166 " pdb=" N LEU A 167 " pdb=" CA LEU A 167 " ideal model delta sigma weight residual 121.03 118.16 2.87 1.60e+00 3.91e-01 3.22e+00 angle pdb=" CA PRO A 184 " pdb=" C PRO A 184 " pdb=" O PRO A 184 " ideal model delta sigma weight residual 123.16 120.49 2.67 1.49e+00 4.50e-01 3.21e+00 angle pdb=" N VAL A 247 " pdb=" CA VAL A 247 " pdb=" C VAL A 247 " ideal model delta sigma weight residual 113.16 110.58 2.58 1.49e+00 4.50e-01 2.99e+00 angle pdb=" N VAL B 247 " pdb=" CA VAL B 247 " pdb=" C VAL B 247 " ideal model delta sigma weight residual 113.16 110.71 2.45 1.49e+00 4.50e-01 2.71e+00 ... (remaining 6504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.75: 2615 13.75 - 27.50: 135 27.50 - 41.26: 40 41.26 - 55.01: 16 55.01 - 68.76: 5 Dihedral angle restraints: 2811 sinusoidal: 1065 harmonic: 1746 Sorted by residual: dihedral pdb=" CA ASN B 53 " pdb=" C ASN B 53 " pdb=" N TYR B 54 " pdb=" CA TYR B 54 " ideal model delta harmonic sigma weight residual 180.00 -162.91 -17.09 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA MET A 264 " pdb=" CB MET A 264 " pdb=" CG MET A 264 " pdb=" SD MET A 264 " ideal model delta sinusoidal sigma weight residual 60.00 119.11 -59.11 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG A 60 " pdb=" CB ARG A 60 " pdb=" CG ARG A 60 " pdb=" CD ARG A 60 " ideal model delta sinusoidal sigma weight residual 180.00 127.49 52.51 3 1.50e+01 4.44e-03 9.12e+00 ... (remaining 2808 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 405 0.023 - 0.046: 184 0.046 - 0.070: 88 0.070 - 0.093: 34 0.093 - 0.116: 29 Chirality restraints: 740 Sorted by residual: chirality pdb=" CA VAL A 35 " pdb=" N VAL A 35 " pdb=" C VAL A 35 " pdb=" CB VAL A 35 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.36e-01 chirality pdb=" CA VAL B 35 " pdb=" N VAL B 35 " pdb=" C VAL B 35 " pdb=" CB VAL B 35 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.14e-01 chirality pdb=" CA ILE A 281 " pdb=" N ILE A 281 " pdb=" C ILE A 281 " pdb=" CB ILE A 281 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.14e-01 ... (remaining 737 not shown) Planarity restraints: 848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 251 " -0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO B 252 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 252 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 252 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 251 " 0.024 5.00e-02 4.00e+02 3.61e-02 2.09e+00 pdb=" N PRO A 252 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 252 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 252 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 38 " -0.018 5.00e-02 4.00e+02 2.74e-02 1.20e+00 pdb=" N PRO B 39 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " -0.015 5.00e-02 4.00e+02 ... (remaining 845 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1520 2.83 - 3.35: 4130 3.35 - 3.87: 7287 3.87 - 4.38: 8302 4.38 - 4.90: 14609 Nonbonded interactions: 35848 Sorted by model distance: nonbonded pdb=" OG SER A 254 " pdb=" O ILE A 259 " model vdw 2.313 2.440 nonbonded pdb=" OH TYR B 209 " pdb=" O ILE B 259 " model vdw 2.341 2.440 nonbonded pdb=" N ASN B 28 " pdb=" OD1 ASN B 28 " model vdw 2.343 2.520 nonbonded pdb=" OD1 ASN A 133 " pdb=" OG1 THR A 135 " model vdw 2.381 2.440 nonbonded pdb=" N ASP B 263 " pdb=" OD1 ASP B 263 " model vdw 2.384 2.520 ... (remaining 35843 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' and (resid 1 through 206 or (resid 207 and (name N or name CA or name \ C or name O or name CB )) or resid 208 through 305)) selection = (chain 'B' and (resid 1 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 305)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 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: 7.060 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 16.730 Find NCS groups from input model: 0.240 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 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 : 0.002 0.039 4785 Z= 0.117 Angle : 0.447 4.222 6509 Z= 0.245 Chirality : 0.038 0.116 740 Planarity : 0.003 0.036 848 Dihedral : 10.502 68.761 1695 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.48 % Favored : 97.19 % Rotamer: Outliers : 2.71 % Allowed : 8.53 % Favored : 88.76 % 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: -0.29 (0.34), residues: 606 helix: 0.58 (0.44), residues: 162 sheet: -0.49 (0.48), residues: 106 loop : -0.40 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 207 HIS 0.002 0.000 HIS B 64 PHE 0.005 0.001 PHE A 230 TYR 0.006 0.001 TYR A 239 ARG 0.001 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 145 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.7014 (ptpt) cc_final: 0.6792 (ptpt) REVERT: A 222 ARG cc_start: 0.5648 (mmm-85) cc_final: 0.5407 (mmm-85) REVERT: B 49 MET cc_start: 0.4720 (tpp) cc_final: 0.4484 (tpp) REVERT: B 93 THR cc_start: 0.8797 (m) cc_final: 0.8574 (p) REVERT: B 222 ARG cc_start: 0.5722 (mmm-85) cc_final: 0.5442 (mmm-85) REVERT: B 238 ASN cc_start: 0.7391 (t0) cc_final: 0.7183 (t0) outliers start: 14 outliers final: 5 residues processed: 156 average time/residue: 0.1909 time to fit residues: 36.5217 Evaluate side-chains 105 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 100 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 263 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 54 optimal weight: 0.0170 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 GLN ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 GLN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 GLN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4785 Z= 0.285 Angle : 0.619 7.024 6509 Z= 0.326 Chirality : 0.044 0.176 740 Planarity : 0.004 0.034 848 Dihedral : 5.226 45.362 659 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.46 % Favored : 95.21 % Rotamer: Outliers : 7.17 % Allowed : 15.70 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.65 (0.33), residues: 606 helix: 0.43 (0.43), residues: 164 sheet: -1.09 (0.50), residues: 82 loop : -0.63 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 207 HIS 0.003 0.001 HIS A 163 PHE 0.026 0.001 PHE A 230 TYR 0.022 0.002 TYR B 239 ARG 0.002 0.000 ARG B 4 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 127 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.8923 (tpp) cc_final: 0.8505 (ttm) REVERT: A 77 VAL cc_start: 0.5658 (OUTLIER) cc_final: 0.5265 (m) REVERT: A 88 LYS cc_start: 0.7089 (ptpt) cc_final: 0.6886 (ptpt) REVERT: A 91 VAL cc_start: 0.4636 (OUTLIER) cc_final: 0.4425 (p) REVERT: A 222 ARG cc_start: 0.5743 (mmm-85) cc_final: 0.5463 (mmm-85) REVERT: B 91 VAL cc_start: 0.4659 (OUTLIER) cc_final: 0.4407 (p) REVERT: B 93 THR cc_start: 0.8787 (m) cc_final: 0.8479 (p) REVERT: B 110 GLN cc_start: 0.8429 (mt0) cc_final: 0.8226 (mt0) REVERT: B 152 ILE cc_start: 0.8786 (tp) cc_final: 0.8542 (mt) REVERT: B 222 ARG cc_start: 0.5895 (mmm-85) cc_final: 0.5591 (mmm-85) REVERT: B 238 ASN cc_start: 0.7605 (t0) cc_final: 0.7380 (t0) REVERT: B 289 ASP cc_start: 0.9160 (p0) cc_final: 0.8913 (p0) outliers start: 37 outliers final: 22 residues processed: 147 average time/residue: 0.1932 time to fit residues: 34.8158 Evaluate side-chains 145 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 120 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 117 CYS Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 263 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 58 optimal weight: 0.0870 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 ASN ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 GLN A 299 GLN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 GLN B 203 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4785 Z= 0.186 Angle : 0.543 5.810 6509 Z= 0.281 Chirality : 0.041 0.132 740 Planarity : 0.004 0.038 848 Dihedral : 5.045 44.868 659 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.80 % Favored : 95.87 % Rotamer: Outliers : 6.20 % Allowed : 18.02 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.34), residues: 606 helix: 0.55 (0.43), residues: 166 sheet: -1.19 (0.45), residues: 90 loop : -0.57 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 207 HIS 0.003 0.001 HIS A 172 PHE 0.012 0.001 PHE A 230 TYR 0.018 0.001 TYR A 239 ARG 0.002 0.000 ARG B 4 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 124 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 VAL cc_start: 0.5710 (OUTLIER) cc_final: 0.5309 (m) REVERT: A 88 LYS cc_start: 0.7061 (ptpt) cc_final: 0.6855 (ptpt) REVERT: A 152 ILE cc_start: 0.8664 (tp) cc_final: 0.8394 (mt) REVERT: A 222 ARG cc_start: 0.5712 (mmm-85) cc_final: 0.5422 (mmm-85) REVERT: B 17 MET cc_start: 0.8782 (tpp) cc_final: 0.8372 (ttp) REVERT: B 93 THR cc_start: 0.8819 (m) cc_final: 0.8593 (p) REVERT: B 102 LYS cc_start: 0.8446 (mmmm) cc_final: 0.8213 (mmmt) REVERT: B 152 ILE cc_start: 0.8780 (tp) cc_final: 0.8498 (mt) REVERT: B 222 ARG cc_start: 0.5875 (mmm-85) cc_final: 0.5547 (mmm-85) REVERT: B 238 ASN cc_start: 0.7484 (t0) cc_final: 0.7038 (t0) outliers start: 32 outliers final: 22 residues processed: 143 average time/residue: 0.1909 time to fit residues: 33.4774 Evaluate side-chains 145 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 122 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 263 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 48 optimal weight: 0.0270 chunk 32 optimal weight: 0.7980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 GLN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 GLN B 299 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4785 Z= 0.183 Angle : 0.561 10.357 6509 Z= 0.282 Chirality : 0.041 0.132 740 Planarity : 0.004 0.047 848 Dihedral : 5.005 44.997 659 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.96 % Favored : 95.71 % Rotamer: Outliers : 6.20 % Allowed : 19.77 % Favored : 74.03 % 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: -0.69 (0.34), residues: 606 helix: 0.61 (0.43), residues: 166 sheet: -1.16 (0.44), residues: 110 loop : -0.70 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 31 HIS 0.003 0.001 HIS A 172 PHE 0.012 0.001 PHE A 230 TYR 0.013 0.001 TYR A 239 ARG 0.002 0.000 ARG B 4 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 128 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 VAL cc_start: 0.5866 (OUTLIER) cc_final: 0.5431 (m) REVERT: A 119 ASN cc_start: 0.8417 (t0) cc_final: 0.8162 (t0) REVERT: A 152 ILE cc_start: 0.8638 (tp) cc_final: 0.8386 (mt) REVERT: A 222 ARG cc_start: 0.5674 (mmm-85) cc_final: 0.5412 (mmm-85) REVERT: B 17 MET cc_start: 0.8664 (tpp) cc_final: 0.8440 (ttp) REVERT: B 93 THR cc_start: 0.8866 (m) cc_final: 0.8645 (p) REVERT: B 110 GLN cc_start: 0.8388 (mt0) cc_final: 0.8178 (mt0) REVERT: B 152 ILE cc_start: 0.8668 (tp) cc_final: 0.8396 (mt) REVERT: B 222 ARG cc_start: 0.5865 (mmm-85) cc_final: 0.5557 (mmm-85) outliers start: 32 outliers final: 27 residues processed: 147 average time/residue: 0.1940 time to fit residues: 35.1364 Evaluate side-chains 151 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 123 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 263 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 0.0670 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4785 Z= 0.235 Angle : 0.598 8.992 6509 Z= 0.307 Chirality : 0.042 0.140 740 Planarity : 0.004 0.046 848 Dihedral : 5.201 46.424 657 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.13 % Favored : 95.54 % Rotamer: Outliers : 5.81 % Allowed : 21.90 % Favored : 72.29 % 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: -0.82 (0.33), residues: 606 helix: 0.53 (0.43), residues: 166 sheet: -1.14 (0.44), residues: 110 loop : -0.83 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 207 HIS 0.003 0.001 HIS A 172 PHE 0.018 0.001 PHE A 230 TYR 0.012 0.001 TYR B 101 ARG 0.004 0.000 ARG B 4 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 125 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 VAL cc_start: 0.5862 (OUTLIER) cc_final: 0.5413 (m) REVERT: A 119 ASN cc_start: 0.8496 (t0) cc_final: 0.8260 (t0) REVERT: A 152 ILE cc_start: 0.8714 (tp) cc_final: 0.8447 (mt) REVERT: A 200 ILE cc_start: 0.8552 (mt) cc_final: 0.8328 (mm) REVERT: A 222 ARG cc_start: 0.5720 (mmm-85) cc_final: 0.5442 (mmm-85) REVERT: B 93 THR cc_start: 0.8871 (m) cc_final: 0.8616 (p) REVERT: B 222 ARG cc_start: 0.5860 (mmm-85) cc_final: 0.5554 (mmm-85) outliers start: 30 outliers final: 26 residues processed: 142 average time/residue: 0.1959 time to fit residues: 34.0482 Evaluate side-chains 151 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 124 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 287 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 GLN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 GLN B 299 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4785 Z= 0.245 Angle : 0.613 8.258 6509 Z= 0.314 Chirality : 0.042 0.159 740 Planarity : 0.004 0.045 848 Dihedral : 5.308 46.880 657 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.13 % Favored : 95.54 % Rotamer: Outliers : 7.56 % Allowed : 20.16 % Favored : 72.29 % 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: -0.94 (0.33), residues: 606 helix: 0.41 (0.42), residues: 166 sheet: -1.18 (0.44), residues: 110 loop : -0.92 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 31 HIS 0.003 0.001 HIS A 172 PHE 0.016 0.001 PHE A 230 TYR 0.010 0.001 TYR A 239 ARG 0.003 0.000 ARG B 4 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 123 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 VAL cc_start: 0.5850 (OUTLIER) cc_final: 0.5405 (m) REVERT: A 119 ASN cc_start: 0.8468 (t0) cc_final: 0.8236 (t0) REVERT: A 152 ILE cc_start: 0.8673 (tp) cc_final: 0.8412 (mt) REVERT: A 200 ILE cc_start: 0.8608 (mt) cc_final: 0.8296 (mm) REVERT: A 222 ARG cc_start: 0.5633 (mmm-85) cc_final: 0.5385 (mmm-85) REVERT: B 93 THR cc_start: 0.8849 (m) cc_final: 0.8600 (p) REVERT: B 222 ARG cc_start: 0.5935 (mmm-85) cc_final: 0.5626 (mmm-85) REVERT: B 279 ARG cc_start: 0.7961 (mtm-85) cc_final: 0.7646 (ttm-80) outliers start: 39 outliers final: 28 residues processed: 149 average time/residue: 0.1875 time to fit residues: 34.3408 Evaluate side-chains 150 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 121 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 287 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.9980 chunk 48 optimal weight: 0.3980 chunk 57 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 HIS ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4785 Z= 0.220 Angle : 0.610 7.602 6509 Z= 0.312 Chirality : 0.042 0.153 740 Planarity : 0.004 0.047 848 Dihedral : 5.255 46.439 657 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.47 % Favored : 96.20 % Rotamer: Outliers : 6.78 % Allowed : 20.54 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.33), residues: 606 helix: 0.45 (0.42), residues: 166 sheet: -1.15 (0.48), residues: 94 loop : -0.92 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 31 HIS 0.003 0.001 HIS B 41 PHE 0.014 0.001 PHE A 230 TYR 0.008 0.001 TYR B 101 ARG 0.003 0.000 ARG B 4 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 122 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.8792 (ttm) cc_final: 0.8551 (ttp) REVERT: A 77 VAL cc_start: 0.5824 (OUTLIER) cc_final: 0.5447 (t) REVERT: A 119 ASN cc_start: 0.8441 (t0) cc_final: 0.8201 (t0) REVERT: A 152 ILE cc_start: 0.8661 (tp) cc_final: 0.8402 (mt) REVERT: A 200 ILE cc_start: 0.8589 (mt) cc_final: 0.8261 (mm) REVERT: A 222 ARG cc_start: 0.5641 (mmm-85) cc_final: 0.5428 (mmm-85) REVERT: B 93 THR cc_start: 0.8850 (m) cc_final: 0.8604 (p) REVERT: B 222 ARG cc_start: 0.5917 (mmm-85) cc_final: 0.5580 (mmm-85) REVERT: B 279 ARG cc_start: 0.7910 (mtm-85) cc_final: 0.7635 (ttm-80) outliers start: 35 outliers final: 29 residues processed: 143 average time/residue: 0.1946 time to fit residues: 33.9773 Evaluate side-chains 151 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 121 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 287 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 GLN ** A 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 HIS ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4785 Z= 0.216 Angle : 0.616 7.197 6509 Z= 0.313 Chirality : 0.042 0.152 740 Planarity : 0.004 0.047 848 Dihedral : 5.210 46.544 657 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.47 % Favored : 96.20 % Rotamer: Outliers : 6.40 % Allowed : 21.71 % Favored : 71.90 % 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: -0.89 (0.33), residues: 606 helix: 0.47 (0.42), residues: 166 sheet: -1.10 (0.47), residues: 94 loop : -0.94 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 31 HIS 0.003 0.001 HIS A 172 PHE 0.013 0.001 PHE A 230 TYR 0.010 0.001 TYR A 239 ARG 0.003 0.000 ARG B 4 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 127 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.8829 (ttm) cc_final: 0.8610 (ttp) REVERT: A 77 VAL cc_start: 0.5834 (OUTLIER) cc_final: 0.5474 (t) REVERT: A 119 ASN cc_start: 0.8458 (t0) cc_final: 0.8215 (t0) REVERT: A 152 ILE cc_start: 0.8663 (tp) cc_final: 0.8394 (mt) REVERT: A 200 ILE cc_start: 0.8598 (mt) cc_final: 0.8312 (mm) REVERT: A 222 ARG cc_start: 0.5633 (mmm-85) cc_final: 0.5396 (mmm-85) REVERT: B 93 THR cc_start: 0.8831 (m) cc_final: 0.8602 (p) REVERT: B 222 ARG cc_start: 0.5926 (mmm-85) cc_final: 0.5602 (mmm-85) REVERT: B 289 ASP cc_start: 0.8914 (p0) cc_final: 0.8614 (p0) outliers start: 33 outliers final: 25 residues processed: 146 average time/residue: 0.1992 time to fit residues: 35.7008 Evaluate side-chains 147 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 121 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 287 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.3980 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 0.0470 chunk 55 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 HIS ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4785 Z= 0.190 Angle : 0.601 6.148 6509 Z= 0.307 Chirality : 0.042 0.145 740 Planarity : 0.004 0.049 848 Dihedral : 5.085 46.540 657 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.30 % Favored : 96.37 % Rotamer: Outliers : 5.43 % Allowed : 22.09 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.34), residues: 606 helix: 0.57 (0.42), residues: 166 sheet: -1.13 (0.47), residues: 94 loop : -0.89 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 31 HIS 0.003 0.001 HIS B 164 PHE 0.010 0.001 PHE A 181 TYR 0.011 0.001 TYR B 101 ARG 0.002 0.000 ARG B 4 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 121 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.8838 (ttm) cc_final: 0.8629 (ttp) REVERT: A 77 VAL cc_start: 0.5832 (OUTLIER) cc_final: 0.5488 (t) REVERT: A 119 ASN cc_start: 0.8433 (t0) cc_final: 0.8189 (t0) REVERT: A 152 ILE cc_start: 0.8621 (tp) cc_final: 0.8369 (mt) REVERT: A 200 ILE cc_start: 0.8567 (mt) cc_final: 0.8257 (mm) REVERT: A 222 ARG cc_start: 0.5631 (mmm-85) cc_final: 0.5405 (mmm-85) REVERT: B 90 LYS cc_start: 0.8108 (ttmm) cc_final: 0.7904 (tttp) REVERT: B 93 THR cc_start: 0.8853 (m) cc_final: 0.8636 (p) REVERT: B 289 ASP cc_start: 0.8904 (p0) cc_final: 0.8603 (p0) outliers start: 28 outliers final: 26 residues processed: 136 average time/residue: 0.1904 time to fit residues: 31.7064 Evaluate side-chains 146 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 119 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 263 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 HIS ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4785 Z= 0.243 Angle : 0.631 6.331 6509 Z= 0.326 Chirality : 0.043 0.156 740 Planarity : 0.004 0.046 848 Dihedral : 5.233 47.278 657 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.63 % Favored : 96.04 % Rotamer: Outliers : 5.62 % Allowed : 22.09 % Favored : 72.29 % 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: -0.66 (0.33), residues: 606 helix: 0.85 (0.43), residues: 154 sheet: -0.59 (0.43), residues: 114 loop : -0.98 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 31 HIS 0.007 0.001 HIS B 164 PHE 0.016 0.001 PHE A 230 TYR 0.011 0.001 TYR B 101 ARG 0.001 0.000 ARG B 188 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 118 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 VAL cc_start: 0.5890 (OUTLIER) cc_final: 0.5561 (t) REVERT: A 119 ASN cc_start: 0.8466 (t0) cc_final: 0.8236 (t0) REVERT: A 152 ILE cc_start: 0.8660 (tp) cc_final: 0.8383 (mt) REVERT: A 222 ARG cc_start: 0.5650 (mmm-85) cc_final: 0.5428 (mmm-85) REVERT: B 93 THR cc_start: 0.8809 (m) cc_final: 0.8584 (p) REVERT: B 289 ASP cc_start: 0.8935 (p0) cc_final: 0.8615 (p0) outliers start: 29 outliers final: 25 residues processed: 135 average time/residue: 0.1864 time to fit residues: 30.9684 Evaluate side-chains 142 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 116 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 263 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.5980 chunk 6 optimal weight: 0.0980 chunk 8 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 38 optimal weight: 0.2980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 HIS ** B 180 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 = 0.4239 r_free = 0.4239 target = 0.161367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.148679 restraints weight = 9711.979| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 3.51 r_work: 0.3958 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4785 Z= 0.203 Angle : 0.642 10.295 6509 Z= 0.323 Chirality : 0.042 0.147 740 Planarity : 0.004 0.048 848 Dihedral : 4.710 33.770 655 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.47 % Favored : 96.20 % Rotamer: Outliers : 5.43 % Allowed : 22.09 % Favored : 72.48 % 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: -0.60 (0.34), residues: 606 helix: 0.96 (0.43), residues: 154 sheet: -0.93 (0.45), residues: 104 loop : -0.83 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 31 HIS 0.005 0.001 HIS B 163 PHE 0.010 0.001 PHE A 230 TYR 0.015 0.001 TYR A 118 ARG 0.002 0.000 ARG B 4 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1570.49 seconds wall clock time: 28 minutes 51.66 seconds (1731.66 seconds total)