Starting phenix.real_space_refine on Wed Feb 14 00:18:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr0_30443/02_2024/7cr0_30443.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr0_30443/02_2024/7cr0_30443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr0_30443/02_2024/7cr0_30443.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr0_30443/02_2024/7cr0_30443.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr0_30443/02_2024/7cr0_30443.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr0_30443/02_2024/7cr0_30443.pdb" } resolution = 3.1 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= 0.003 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 36 5.16 5 C 5436 2.51 5 N 1380 2.21 5 O 1336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 117": "OE1" <-> "OE2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B GLU 257": "OE1" <-> "OE2" Residue "B GLU 322": "OE1" <-> "OE2" Residue "B GLU 330": "OE1" <-> "OE2" Residue "C GLU 117": "OE1" <-> "OE2" Residue "C GLU 257": "OE1" <-> "OE2" Residue "C GLU 322": "OE1" <-> "OE2" Residue "C GLU 330": "OE1" <-> "OE2" Residue "D GLU 117": "OE1" <-> "OE2" Residue "D GLU 257": "OE1" <-> "OE2" Residue "D GLU 322": "OE1" <-> "OE2" Residue "D GLU 330": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8188 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2047 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 Chain: "B" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2047 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 Chain: "C" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2047 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 Chain: "D" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2047 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 Time building chain proxies: 4.81, per 1000 atoms: 0.59 Number of scatterers: 8188 At special positions: 0 Unit cell: (132.834, 132.834, 77.064, 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 36 16.00 O 1336 8.00 N 1380 7.00 C 5436 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: 2.95 Conformation dependent library (CDL) restraints added in 1.4 seconds 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1856 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 0 sheets defined 85.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 70 through 86 Processing helix chain 'A' and resid 91 through 114 removed outlier: 4.178A pdb=" N TYR A 95 " --> pdb=" O TRP A 91 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 148 removed outlier: 4.715A pdb=" N ILE A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 165 Processing helix chain 'A' and resid 166 through 183 Processing helix chain 'A' and resid 196 through 211 Processing helix chain 'A' and resid 215 through 228 Processing helix chain 'A' and resid 228 through 254 Processing helix chain 'A' and resid 263 through 276 removed outlier: 3.570A pdb=" N ALA A 267 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 330 removed outlier: 3.718A pdb=" N ARG A 291 " --> pdb=" O THR A 287 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Proline residue: A 308 - end of helix removed outlier: 4.105A pdb=" N GLU A 330 " --> pdb=" O GLN A 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 86 Processing helix chain 'B' and resid 91 through 114 removed outlier: 4.178A pdb=" N TYR B 95 " --> pdb=" O TRP B 91 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 148 removed outlier: 4.715A pdb=" N ILE B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 165 Processing helix chain 'B' and resid 166 through 183 Processing helix chain 'B' and resid 196 through 211 Processing helix chain 'B' and resid 215 through 228 Processing helix chain 'B' and resid 228 through 254 Processing helix chain 'B' and resid 263 through 276 removed outlier: 3.570A pdb=" N ALA B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR B 276 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 330 removed outlier: 3.718A pdb=" N ARG B 291 " --> pdb=" O THR B 287 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Proline residue: B 308 - end of helix removed outlier: 4.105A pdb=" N GLU B 330 " --> pdb=" O GLN B 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 86 Processing helix chain 'C' and resid 91 through 114 removed outlier: 4.177A pdb=" N TYR C 95 " --> pdb=" O TRP C 91 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 148 removed outlier: 4.715A pdb=" N ILE C 128 " --> pdb=" O GLY C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 165 Processing helix chain 'C' and resid 166 through 183 Processing helix chain 'C' and resid 196 through 211 Processing helix chain 'C' and resid 215 through 228 Processing helix chain 'C' and resid 228 through 254 Processing helix chain 'C' and resid 263 through 276 removed outlier: 3.570A pdb=" N ALA C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR C 276 " --> pdb=" O LEU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 330 removed outlier: 3.718A pdb=" N ARG C 291 " --> pdb=" O THR C 287 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Proline residue: C 308 - end of helix removed outlier: 4.105A pdb=" N GLU C 330 " --> pdb=" O GLN C 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 86 Processing helix chain 'D' and resid 91 through 114 removed outlier: 4.178A pdb=" N TYR D 95 " --> pdb=" O TRP D 91 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR D 114 " --> pdb=" O SER D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 148 removed outlier: 4.715A pdb=" N ILE D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 165 Processing helix chain 'D' and resid 166 through 183 Processing helix chain 'D' and resid 196 through 211 Processing helix chain 'D' and resid 215 through 228 Processing helix chain 'D' and resid 228 through 254 Processing helix chain 'D' and resid 263 through 276 removed outlier: 3.570A pdb=" N ALA D 267 " --> pdb=" O THR D 263 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR D 276 " --> pdb=" O LEU D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 330 removed outlier: 3.718A pdb=" N ARG D 291 " --> pdb=" O THR D 287 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU D 299 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Proline residue: D 308 - end of helix removed outlier: 4.105A pdb=" N GLU D 330 " --> pdb=" O GLN D 326 " (cutoff:3.500A) 645 hydrogen bonds defined for protein. 1935 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: 2.16 Time building geometry restraints manager: 3.20 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: 2480 1.34 - 1.46: 2350 1.46 - 1.58: 3534 1.58 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 8412 Sorted by residual: bond pdb=" CD2 TYR B 280 " pdb=" CE2 TYR B 280 " ideal model delta sigma weight residual 1.382 1.352 0.030 3.00e-02 1.11e+03 9.69e-01 bond pdb=" CD2 TYR D 280 " pdb=" CE2 TYR D 280 " ideal model delta sigma weight residual 1.382 1.352 0.030 3.00e-02 1.11e+03 9.69e-01 bond pdb=" CD2 TYR A 280 " pdb=" CE2 TYR A 280 " ideal model delta sigma weight residual 1.382 1.352 0.030 3.00e-02 1.11e+03 9.69e-01 bond pdb=" CD2 TYR C 280 " pdb=" CE2 TYR C 280 " ideal model delta sigma weight residual 1.382 1.352 0.030 3.00e-02 1.11e+03 9.69e-01 bond pdb=" CB THR C 274 " pdb=" CG2 THR C 274 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.60e-01 ... (remaining 8407 not shown) Histogram of bond angle deviations from ideal: 99.11 - 106.10: 72 106.10 - 113.08: 4504 113.08 - 120.07: 3608 120.07 - 127.06: 3100 127.06 - 134.04: 104 Bond angle restraints: 11388 Sorted by residual: angle pdb=" N ARG B 87 " pdb=" CA ARG B 87 " pdb=" C ARG B 87 " ideal model delta sigma weight residual 109.81 114.52 -4.71 2.21e+00 2.05e-01 4.54e+00 angle pdb=" N ARG C 87 " pdb=" CA ARG C 87 " pdb=" C ARG C 87 " ideal model delta sigma weight residual 109.81 114.52 -4.71 2.21e+00 2.05e-01 4.54e+00 angle pdb=" N ARG D 87 " pdb=" CA ARG D 87 " pdb=" C ARG D 87 " ideal model delta sigma weight residual 109.81 114.52 -4.71 2.21e+00 2.05e-01 4.54e+00 angle pdb=" N ARG A 87 " pdb=" CA ARG A 87 " pdb=" C ARG A 87 " ideal model delta sigma weight residual 109.81 114.52 -4.71 2.21e+00 2.05e-01 4.54e+00 angle pdb=" C ASP A 212 " pdb=" N ARG A 213 " pdb=" CA ARG A 213 " ideal model delta sigma weight residual 121.54 125.46 -3.92 1.91e+00 2.74e-01 4.22e+00 ... (remaining 11383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 4272 17.87 - 35.74: 428 35.74 - 53.61: 80 53.61 - 71.48: 8 71.48 - 89.35: 4 Dihedral angle restraints: 4792 sinusoidal: 1884 harmonic: 2908 Sorted by residual: dihedral pdb=" CA GLU A 86 " pdb=" C GLU A 86 " pdb=" N ARG A 87 " pdb=" CA ARG A 87 " ideal model delta harmonic sigma weight residual -180.00 -160.39 -19.61 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA GLU D 86 " pdb=" C GLU D 86 " pdb=" N ARG D 87 " pdb=" CA ARG D 87 " ideal model delta harmonic sigma weight residual 180.00 -160.42 -19.58 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA GLU C 86 " pdb=" C GLU C 86 " pdb=" N ARG C 87 " pdb=" CA ARG C 87 " ideal model delta harmonic sigma weight residual 180.00 -160.42 -19.58 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 4789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 712 0.031 - 0.063: 422 0.063 - 0.094: 90 0.094 - 0.125: 20 0.125 - 0.157: 8 Chirality restraints: 1252 Sorted by residual: chirality pdb=" CA ARG B 87 " pdb=" N ARG B 87 " pdb=" C ARG B 87 " pdb=" CB ARG B 87 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.14e-01 chirality pdb=" CA ARG C 87 " pdb=" N ARG C 87 " pdb=" C ARG C 87 " pdb=" CB ARG C 87 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.14e-01 chirality pdb=" CA ARG D 87 " pdb=" N ARG D 87 " pdb=" C ARG D 87 " pdb=" CB ARG D 87 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.14e-01 ... (remaining 1249 not shown) Planarity restraints: 1380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 298 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C THR A 298 " -0.028 2.00e-02 2.50e+03 pdb=" O THR A 298 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU A 299 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 298 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C THR D 298 " -0.028 2.00e-02 2.50e+03 pdb=" O THR D 298 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU D 299 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 298 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C THR B 298 " 0.028 2.00e-02 2.50e+03 pdb=" O THR B 298 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU B 299 " -0.009 2.00e-02 2.50e+03 ... (remaining 1377 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1403 2.75 - 3.29: 7751 3.29 - 3.82: 13206 3.82 - 4.36: 15284 4.36 - 4.90: 26020 Nonbonded interactions: 63664 Sorted by model distance: nonbonded pdb=" OE1 GLU C 86 " pdb=" NH2 ARG C 214 " model vdw 2.212 2.520 nonbonded pdb=" OE1 GLU D 86 " pdb=" NH2 ARG D 214 " model vdw 2.212 2.520 nonbonded pdb=" OE1 GLU A 86 " pdb=" NH2 ARG A 214 " model vdw 2.212 2.520 nonbonded pdb=" OE1 GLU B 86 " pdb=" NH2 ARG B 214 " model vdw 2.212 2.520 nonbonded pdb=" O SER B 110 " pdb=" NH2 ARG B 201 " model vdw 2.262 2.520 ... (remaining 63659 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' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.600 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: 3.360 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 24.350 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 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 : 0.005 0.032 8412 Z= 0.327 Angle : 0.627 5.250 11388 Z= 0.378 Chirality : 0.040 0.157 1252 Planarity : 0.005 0.029 1380 Dihedral : 14.379 89.345 2936 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % 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: -4.99 (0.17), residues: 988 helix: -2.96 (0.11), residues: 824 sheet: None (None), residues: 0 loop : -3.65 (0.39), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 269 HIS 0.003 0.001 HIS A 96 PHE 0.013 0.001 PHE B 73 TYR 0.024 0.002 TYR C 98 ARG 0.004 0.001 ARG D 201 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 0.890 Fit side-chains REVERT: A 78 GLN cc_start: 0.7956 (tt0) cc_final: 0.7568 (tt0) REVERT: B 78 GLN cc_start: 0.7954 (tt0) cc_final: 0.7568 (tt0) REVERT: C 78 GLN cc_start: 0.7953 (tt0) cc_final: 0.7569 (tt0) REVERT: D 78 GLN cc_start: 0.7954 (tt0) cc_final: 0.7568 (tt0) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2290 time to fit residues: 50.2570 Evaluate side-chains 150 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 HIS A 323 GLN ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 HIS B 323 GLN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 HIS C 323 GLN ** C 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 HIS D 323 GLN ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 8412 Z= 0.177 Angle : 0.514 5.251 11388 Z= 0.287 Chirality : 0.036 0.114 1252 Planarity : 0.004 0.024 1380 Dihedral : 4.213 12.808 1124 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.86 % Allowed : 14.05 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.24), residues: 988 helix: 0.03 (0.16), residues: 824 sheet: None (None), residues: 0 loop : -2.90 (0.40), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 146 HIS 0.002 0.001 HIS B 328 PHE 0.013 0.002 PHE A 163 TYR 0.012 0.002 TYR B 280 ARG 0.002 0.000 ARG D 201 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 171 time to evaluate : 1.058 Fit side-chains REVERT: A 78 GLN cc_start: 0.7848 (tt0) cc_final: 0.7613 (tt0) REVERT: A 102 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7832 (tp) REVERT: A 129 LEU cc_start: 0.8254 (tp) cc_final: 0.7877 (tt) REVERT: A 202 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.7803 (t80) REVERT: B 78 GLN cc_start: 0.7826 (tt0) cc_final: 0.7570 (tt0) REVERT: B 102 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7832 (tp) REVERT: B 129 LEU cc_start: 0.8250 (tp) cc_final: 0.7870 (tt) REVERT: B 202 PHE cc_start: 0.8079 (OUTLIER) cc_final: 0.7807 (t80) REVERT: C 78 GLN cc_start: 0.7828 (tt0) cc_final: 0.7575 (tt0) REVERT: C 102 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7846 (tp) REVERT: C 129 LEU cc_start: 0.8261 (tp) cc_final: 0.7877 (tt) REVERT: C 202 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7812 (t80) REVERT: D 78 GLN cc_start: 0.7830 (tt0) cc_final: 0.7576 (tt0) REVERT: D 102 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7837 (tp) REVERT: D 129 LEU cc_start: 0.8253 (tp) cc_final: 0.7872 (tt) REVERT: D 202 PHE cc_start: 0.8080 (OUTLIER) cc_final: 0.7803 (t80) outliers start: 24 outliers final: 16 residues processed: 183 average time/residue: 0.1882 time to fit residues: 47.1731 Evaluate side-chains 184 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 160 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 202 PHE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 202 PHE Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 320 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 GLN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 GLN ** C 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 GLN ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 8412 Z= 0.193 Angle : 0.485 5.088 11388 Z= 0.266 Chirality : 0.036 0.121 1252 Planarity : 0.003 0.023 1380 Dihedral : 3.853 11.968 1124 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.21 % Allowed : 17.38 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.26), residues: 988 helix: 1.27 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -2.86 (0.42), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 146 HIS 0.002 0.001 HIS B 96 PHE 0.008 0.001 PHE A 240 TYR 0.010 0.001 TYR A 237 ARG 0.002 0.000 ARG C 207 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 160 time to evaluate : 0.941 Fit side-chains REVERT: A 78 GLN cc_start: 0.7899 (tt0) cc_final: 0.7572 (tt0) REVERT: A 129 LEU cc_start: 0.8256 (tp) cc_final: 0.7909 (tt) REVERT: A 202 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.7896 (t80) REVERT: B 78 GLN cc_start: 0.7962 (tt0) cc_final: 0.7600 (tt0) REVERT: B 129 LEU cc_start: 0.8252 (tp) cc_final: 0.7904 (tt) REVERT: B 202 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.7900 (t80) REVERT: C 78 GLN cc_start: 0.7965 (tt0) cc_final: 0.7605 (tt0) REVERT: C 129 LEU cc_start: 0.8261 (tp) cc_final: 0.7894 (tt) REVERT: C 202 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7905 (t80) REVERT: D 78 GLN cc_start: 0.7965 (tt0) cc_final: 0.7609 (tt0) REVERT: D 129 LEU cc_start: 0.8253 (tp) cc_final: 0.7887 (tt) REVERT: D 202 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7900 (t80) outliers start: 27 outliers final: 19 residues processed: 176 average time/residue: 0.1808 time to fit residues: 44.1948 Evaluate side-chains 172 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 149 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 202 PHE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 202 PHE Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 329 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 86 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 GLN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 GLN ** C 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 GLN ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 8412 Z= 0.173 Angle : 0.476 5.577 11388 Z= 0.254 Chirality : 0.035 0.114 1252 Planarity : 0.003 0.022 1380 Dihedral : 3.681 11.379 1124 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.81 % Allowed : 16.43 % Favored : 79.76 % 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: 1.74 (0.27), residues: 988 helix: 1.83 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -2.71 (0.42), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 146 HIS 0.002 0.001 HIS C 96 PHE 0.013 0.001 PHE A 137 TYR 0.010 0.001 TYR C 237 ARG 0.004 0.000 ARG C 207 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 158 time to evaluate : 0.950 Fit side-chains REVERT: A 78 GLN cc_start: 0.7898 (tt0) cc_final: 0.7595 (tt0) REVERT: A 129 LEU cc_start: 0.8172 (tp) cc_final: 0.7791 (tt) REVERT: A 202 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.7869 (t80) REVERT: B 78 GLN cc_start: 0.7853 (tt0) cc_final: 0.7595 (tt0) REVERT: B 129 LEU cc_start: 0.8167 (tp) cc_final: 0.7785 (tt) REVERT: B 202 PHE cc_start: 0.8165 (OUTLIER) cc_final: 0.7873 (t80) REVERT: C 78 GLN cc_start: 0.7848 (tt0) cc_final: 0.7593 (tt0) REVERT: C 129 LEU cc_start: 0.8172 (tp) cc_final: 0.7794 (tt) REVERT: C 202 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7885 (t80) REVERT: D 78 GLN cc_start: 0.7850 (tt0) cc_final: 0.7593 (tt0) REVERT: D 129 LEU cc_start: 0.8161 (tp) cc_final: 0.7785 (tt) REVERT: D 202 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7895 (t80) outliers start: 32 outliers final: 19 residues processed: 178 average time/residue: 0.1718 time to fit residues: 43.4940 Evaluate side-chains 177 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 154 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 202 PHE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 202 PHE Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 329 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 82 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN B 323 GLN C 323 GLN D 323 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 8412 Z= 0.157 Angle : 0.454 4.933 11388 Z= 0.245 Chirality : 0.035 0.112 1252 Planarity : 0.002 0.027 1380 Dihedral : 3.558 11.119 1124 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.05 % Allowed : 17.74 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.27), residues: 988 helix: 2.17 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -2.65 (0.42), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 146 HIS 0.002 0.001 HIS B 96 PHE 0.012 0.001 PHE A 137 TYR 0.010 0.001 TYR D 237 ARG 0.007 0.000 ARG C 207 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 151 time to evaluate : 0.962 Fit side-chains REVERT: A 78 GLN cc_start: 0.7843 (tt0) cc_final: 0.7615 (tt0) REVERT: A 129 LEU cc_start: 0.8171 (tp) cc_final: 0.7913 (tp) REVERT: A 202 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7891 (t80) REVERT: B 78 GLN cc_start: 0.7826 (tt0) cc_final: 0.7578 (tt0) REVERT: B 129 LEU cc_start: 0.8164 (tp) cc_final: 0.7906 (tp) REVERT: B 202 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7895 (t80) REVERT: C 78 GLN cc_start: 0.7823 (tt0) cc_final: 0.7577 (tt0) REVERT: C 129 LEU cc_start: 0.8167 (tp) cc_final: 0.7919 (tp) REVERT: C 202 PHE cc_start: 0.8165 (OUTLIER) cc_final: 0.7909 (t80) REVERT: D 78 GLN cc_start: 0.7823 (tt0) cc_final: 0.7579 (tt0) REVERT: D 129 LEU cc_start: 0.8156 (tp) cc_final: 0.7885 (tp) REVERT: D 202 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.7903 (t80) outliers start: 34 outliers final: 19 residues processed: 173 average time/residue: 0.1751 time to fit residues: 42.3953 Evaluate side-chains 173 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 150 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 202 PHE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 202 PHE Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 329 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 8 optimal weight: 9.9990 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN B 323 GLN C 323 GLN D 323 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 8412 Z= 0.156 Angle : 0.466 7.142 11388 Z= 0.244 Chirality : 0.035 0.113 1252 Planarity : 0.002 0.020 1380 Dihedral : 3.492 10.807 1124 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.05 % Allowed : 17.38 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.27), residues: 988 helix: 2.37 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -2.54 (0.43), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 146 HIS 0.002 0.001 HIS D 96 PHE 0.011 0.001 PHE A 137 TYR 0.010 0.001 TYR C 237 ARG 0.004 0.000 ARG A 210 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 149 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLN cc_start: 0.7855 (tt0) cc_final: 0.7632 (tt0) REVERT: A 129 LEU cc_start: 0.8159 (tp) cc_final: 0.7913 (tp) REVERT: A 202 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7897 (t80) REVERT: B 129 LEU cc_start: 0.8152 (tp) cc_final: 0.7888 (tp) REVERT: B 202 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7898 (t80) REVERT: B 322 GLU cc_start: 0.8144 (pp20) cc_final: 0.7928 (pp20) REVERT: C 129 LEU cc_start: 0.8145 (tp) cc_final: 0.7899 (tp) REVERT: C 202 PHE cc_start: 0.8150 (OUTLIER) cc_final: 0.7898 (t80) REVERT: C 322 GLU cc_start: 0.8142 (pp20) cc_final: 0.7927 (pp20) REVERT: D 129 LEU cc_start: 0.8163 (tp) cc_final: 0.7891 (tp) REVERT: D 202 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7900 (t80) outliers start: 34 outliers final: 19 residues processed: 171 average time/residue: 0.1864 time to fit residues: 44.3799 Evaluate side-chains 167 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 144 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 202 PHE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 202 PHE Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 329 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 0.0670 chunk 57 optimal weight: 4.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN B 323 GLN C 323 GLN D 323 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 8412 Z= 0.171 Angle : 0.483 8.472 11388 Z= 0.250 Chirality : 0.035 0.114 1252 Planarity : 0.002 0.019 1380 Dihedral : 3.481 10.580 1124 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.45 % Allowed : 17.86 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.27), residues: 988 helix: 2.46 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -2.43 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 146 HIS 0.002 0.001 HIS D 96 PHE 0.010 0.001 PHE A 137 TYR 0.010 0.001 TYR D 237 ARG 0.002 0.000 ARG A 210 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 149 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.8177 (tp) cc_final: 0.7928 (tp) REVERT: A 202 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7893 (t80) REVERT: B 129 LEU cc_start: 0.8166 (tp) cc_final: 0.7918 (tp) REVERT: B 202 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7896 (t80) REVERT: B 322 GLU cc_start: 0.8146 (pp20) cc_final: 0.7918 (pp20) REVERT: C 129 LEU cc_start: 0.8170 (tp) cc_final: 0.7923 (tp) REVERT: D 129 LEU cc_start: 0.8152 (tp) cc_final: 0.7906 (tp) REVERT: D 202 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7904 (t80) outliers start: 29 outliers final: 23 residues processed: 167 average time/residue: 0.1755 time to fit residues: 40.7057 Evaluate side-chains 171 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 145 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 202 PHE Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 329 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.3980 chunk 18 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 323 GLN B 79 ASN B 323 GLN C 79 ASN C 323 GLN D 79 ASN D 323 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8412 Z= 0.148 Angle : 0.477 9.598 11388 Z= 0.244 Chirality : 0.035 0.111 1252 Planarity : 0.002 0.019 1380 Dihedral : 3.427 10.393 1124 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.57 % Allowed : 17.14 % Favored : 79.29 % 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: 2.72 (0.27), residues: 988 helix: 2.51 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -2.41 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 146 HIS 0.002 0.001 HIS A 96 PHE 0.010 0.001 PHE A 137 TYR 0.010 0.001 TYR D 237 ARG 0.004 0.000 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 151 time to evaluate : 0.844 Fit side-chains REVERT: A 129 LEU cc_start: 0.8144 (tp) cc_final: 0.7876 (tp) REVERT: A 202 PHE cc_start: 0.8150 (OUTLIER) cc_final: 0.7890 (t80) REVERT: A 322 GLU cc_start: 0.8119 (pp20) cc_final: 0.7912 (pp20) REVERT: B 78 GLN cc_start: 0.7797 (tt0) cc_final: 0.7588 (tt0) REVERT: B 129 LEU cc_start: 0.8143 (tp) cc_final: 0.7898 (tp) REVERT: B 202 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.7894 (t80) REVERT: B 322 GLU cc_start: 0.8124 (pp20) cc_final: 0.7919 (pp20) REVERT: C 78 GLN cc_start: 0.7802 (tt0) cc_final: 0.7593 (tt0) REVERT: C 129 LEU cc_start: 0.8138 (tp) cc_final: 0.7903 (tp) REVERT: C 322 GLU cc_start: 0.8070 (pp20) cc_final: 0.7867 (pp20) REVERT: D 78 GLN cc_start: 0.7800 (tt0) cc_final: 0.7595 (tt0) REVERT: D 129 LEU cc_start: 0.8153 (tp) cc_final: 0.7907 (tp) REVERT: D 202 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.7910 (t80) REVERT: D 322 GLU cc_start: 0.8065 (pp20) cc_final: 0.7860 (pp20) outliers start: 30 outliers final: 24 residues processed: 170 average time/residue: 0.1945 time to fit residues: 45.2450 Evaluate side-chains 175 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 148 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 202 PHE Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 329 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 94 optimal weight: 0.6980 chunk 57 optimal weight: 0.0980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN B 323 GLN C 323 GLN D 323 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8412 Z= 0.146 Angle : 0.480 9.301 11388 Z= 0.246 Chirality : 0.035 0.112 1252 Planarity : 0.002 0.020 1380 Dihedral : 3.402 10.547 1124 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.57 % Allowed : 17.02 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.79 (0.27), residues: 988 helix: 2.55 (0.17), residues: 832 sheet: None (None), residues: 0 loop : -2.36 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 146 HIS 0.002 0.001 HIS B 96 PHE 0.013 0.001 PHE D 137 TYR 0.010 0.001 TYR A 74 ARG 0.005 0.000 ARG D 207 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 150 time to evaluate : 1.027 Fit side-chains REVERT: A 129 LEU cc_start: 0.8144 (tp) cc_final: 0.7899 (tp) REVERT: A 202 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7893 (t80) REVERT: A 322 GLU cc_start: 0.8125 (pp20) cc_final: 0.7908 (pp20) REVERT: B 78 GLN cc_start: 0.7814 (tt0) cc_final: 0.7591 (tt0) REVERT: B 129 LEU cc_start: 0.8136 (tp) cc_final: 0.7906 (tp) REVERT: B 202 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7898 (t80) REVERT: B 322 GLU cc_start: 0.8121 (pp20) cc_final: 0.7904 (pp20) REVERT: C 78 GLN cc_start: 0.7819 (tt0) cc_final: 0.7617 (tt0) REVERT: C 129 LEU cc_start: 0.8160 (tp) cc_final: 0.7931 (tp) REVERT: C 322 GLU cc_start: 0.8066 (pp20) cc_final: 0.7852 (pp20) REVERT: D 129 LEU cc_start: 0.8143 (tp) cc_final: 0.7899 (tp) REVERT: D 202 PHE cc_start: 0.8149 (OUTLIER) cc_final: 0.7915 (t80) REVERT: D 322 GLU cc_start: 0.8069 (pp20) cc_final: 0.7860 (pp20) outliers start: 30 outliers final: 26 residues processed: 169 average time/residue: 0.1992 time to fit residues: 46.1550 Evaluate side-chains 179 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 150 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 202 PHE Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 329 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 8 optimal weight: 0.0870 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 84 optimal weight: 0.0020 chunk 24 optimal weight: 4.9990 overall best weight: 0.7968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN B 323 GLN C 323 GLN ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8412 Z= 0.154 Angle : 0.495 9.372 11388 Z= 0.250 Chirality : 0.035 0.111 1252 Planarity : 0.002 0.027 1380 Dihedral : 3.404 10.632 1124 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.33 % Allowed : 16.90 % Favored : 79.76 % 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: 2.83 (0.27), residues: 988 helix: 2.58 (0.17), residues: 832 sheet: None (None), residues: 0 loop : -2.36 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 146 HIS 0.002 0.001 HIS C 96 PHE 0.023 0.001 PHE D 137 TYR 0.011 0.001 TYR D 74 ARG 0.011 0.000 ARG D 207 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 150 time to evaluate : 0.935 Fit side-chains REVERT: A 129 LEU cc_start: 0.8146 (tp) cc_final: 0.7901 (tp) REVERT: A 202 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.7894 (t80) REVERT: A 322 GLU cc_start: 0.8123 (pp20) cc_final: 0.7904 (pp20) REVERT: B 78 GLN cc_start: 0.7811 (tt0) cc_final: 0.7611 (tt0) REVERT: B 129 LEU cc_start: 0.8140 (tp) cc_final: 0.7897 (tp) REVERT: B 202 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7900 (t80) REVERT: B 322 GLU cc_start: 0.8119 (pp20) cc_final: 0.7900 (pp20) REVERT: C 78 GLN cc_start: 0.7812 (tt0) cc_final: 0.7611 (tt0) REVERT: C 129 LEU cc_start: 0.8145 (tp) cc_final: 0.7931 (tp) REVERT: C 322 GLU cc_start: 0.8063 (pp20) cc_final: 0.7846 (pp20) REVERT: D 129 LEU cc_start: 0.8157 (tp) cc_final: 0.7911 (tp) REVERT: D 202 PHE cc_start: 0.8151 (OUTLIER) cc_final: 0.7912 (t80) REVERT: D 322 GLU cc_start: 0.8064 (pp20) cc_final: 0.7848 (pp20) outliers start: 28 outliers final: 25 residues processed: 167 average time/residue: 0.1915 time to fit residues: 44.3210 Evaluate side-chains 176 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 148 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 202 PHE Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 329 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 3.9990 chunk 11 optimal weight: 0.0170 chunk 22 optimal weight: 0.0970 chunk 79 optimal weight: 0.2980 chunk 33 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN B 323 GLN C 323 GLN ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.163159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.116963 restraints weight = 10139.924| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.93 r_work: 0.3293 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8412 Z= 0.128 Angle : 0.479 9.346 11388 Z= 0.243 Chirality : 0.034 0.107 1252 Planarity : 0.002 0.023 1380 Dihedral : 3.327 10.399 1124 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.33 % Allowed : 17.50 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.95 (0.27), residues: 988 helix: 2.66 (0.17), residues: 832 sheet: None (None), residues: 0 loop : -2.32 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 146 HIS 0.001 0.000 HIS B 96 PHE 0.023 0.001 PHE D 137 TYR 0.010 0.001 TYR D 237 ARG 0.011 0.000 ARG D 207 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2041.26 seconds wall clock time: 37 minutes 38.59 seconds (2258.59 seconds total)