Starting phenix.real_space_refine on Thu Feb 15 16:28:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d63_27215/02_2024/8d63_27215_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d63_27215/02_2024/8d63_27215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d63_27215/02_2024/8d63_27215.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d63_27215/02_2024/8d63_27215.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d63_27215/02_2024/8d63_27215_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d63_27215/02_2024/8d63_27215_updated.pdb" } resolution = 3.14 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= 0.012 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: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 30 5.16 5 C 8375 2.51 5 N 2085 2.21 5 O 2290 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 30": "OE1" <-> "OE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B GLU 292": "OE1" <-> "OE2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D GLU 159": "OE1" <-> "OE2" Residue "D GLU 292": "OE1" <-> "OE2" Residue "E GLU 30": "OE1" <-> "OE2" Residue "E GLU 159": "OE1" <-> "OE2" Residue "E GLU 292": "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: 12785 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "B" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "C" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "D" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "E" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'LBN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'LBN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'LBN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'LBN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'LBN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.91, per 1000 atoms: 0.54 Number of scatterers: 12785 At special positions: 0 Unit cell: (92.4, 91.3, 122.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 5 15.00 O 2290 8.00 N 2085 7.00 C 8375 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: 4.83 Conformation dependent library (CDL) restraints added in 2.2 seconds 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2910 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 20 sheets defined 30.3% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 176 through 179 removed outlier: 3.697A pdb=" N SER A 179 " --> pdb=" O ASP A 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 176 through 179' Processing helix chain 'A' and resid 202 through 207 Processing helix chain 'A' and resid 209 through 220 removed outlier: 3.695A pdb=" N TRP A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 251 Processing helix chain 'A' and resid 261 through 285 Processing helix chain 'A' and resid 297 through 299 No H-bonds generated for 'chain 'A' and resid 297 through 299' Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'B' and resid 62 through 68 Processing helix chain 'B' and resid 176 through 179 removed outlier: 3.697A pdb=" N SER B 179 " --> pdb=" O ASP B 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 176 through 179' Processing helix chain 'B' and resid 202 through 207 Processing helix chain 'B' and resid 209 through 220 removed outlier: 3.695A pdb=" N TRP B 220 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 251 Processing helix chain 'B' and resid 261 through 285 Processing helix chain 'B' and resid 297 through 299 No H-bonds generated for 'chain 'B' and resid 297 through 299' Processing helix chain 'B' and resid 304 through 316 Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 176 through 179 removed outlier: 3.697A pdb=" N SER C 179 " --> pdb=" O ASP C 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 176 through 179' Processing helix chain 'C' and resid 202 through 207 Processing helix chain 'C' and resid 209 through 220 removed outlier: 3.694A pdb=" N TRP C 220 " --> pdb=" O ILE C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 251 Processing helix chain 'C' and resid 261 through 285 Processing helix chain 'C' and resid 297 through 299 No H-bonds generated for 'chain 'C' and resid 297 through 299' Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'D' and resid 62 through 68 Processing helix chain 'D' and resid 176 through 179 removed outlier: 3.697A pdb=" N SER D 179 " --> pdb=" O ASP D 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 176 through 179' Processing helix chain 'D' and resid 202 through 207 Processing helix chain 'D' and resid 209 through 220 removed outlier: 3.695A pdb=" N TRP D 220 " --> pdb=" O ILE D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 251 Processing helix chain 'D' and resid 261 through 285 Processing helix chain 'D' and resid 297 through 299 No H-bonds generated for 'chain 'D' and resid 297 through 299' Processing helix chain 'D' and resid 304 through 316 Processing helix chain 'E' and resid 62 through 68 Processing helix chain 'E' and resid 176 through 179 removed outlier: 3.697A pdb=" N SER E 179 " --> pdb=" O ASP E 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 176 through 179' Processing helix chain 'E' and resid 202 through 207 Processing helix chain 'E' and resid 209 through 220 removed outlier: 3.694A pdb=" N TRP E 220 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 251 Processing helix chain 'E' and resid 261 through 285 Processing helix chain 'E' and resid 297 through 299 No H-bonds generated for 'chain 'E' and resid 297 through 299' Processing helix chain 'E' and resid 304 through 316 Processing sheet with id= A, first strand: chain 'A' and resid 12 through 14 Processing sheet with id= B, first strand: chain 'A' and resid 145 through 148 removed outlier: 6.844A pdb=" N VAL A 16 " --> pdb=" O GLN A 146 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N TYR A 148 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE A 18 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP A 36 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE A 23 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LYS A 34 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 76 through 78 Processing sheet with id= D, first strand: chain 'A' and resid 167 through 174 Processing sheet with id= E, first strand: chain 'B' and resid 12 through 14 Processing sheet with id= F, first strand: chain 'B' and resid 145 through 148 removed outlier: 6.844A pdb=" N VAL B 16 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N TYR B 148 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE B 18 " --> pdb=" O TYR B 148 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP B 36 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE B 23 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LYS B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 76 through 78 Processing sheet with id= H, first strand: chain 'B' and resid 167 through 174 Processing sheet with id= I, first strand: chain 'C' and resid 12 through 14 Processing sheet with id= J, first strand: chain 'C' and resid 145 through 148 removed outlier: 6.844A pdb=" N VAL C 16 " --> pdb=" O GLN C 146 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N TYR C 148 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE C 18 " --> pdb=" O TYR C 148 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP C 36 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE C 23 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LYS C 34 " --> pdb=" O ILE C 23 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 76 through 78 Processing sheet with id= L, first strand: chain 'C' and resid 167 through 174 Processing sheet with id= M, first strand: chain 'D' and resid 12 through 14 Processing sheet with id= N, first strand: chain 'D' and resid 145 through 148 removed outlier: 6.844A pdb=" N VAL D 16 " --> pdb=" O GLN D 146 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N TYR D 148 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE D 18 " --> pdb=" O TYR D 148 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASP D 36 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE D 23 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LYS D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 76 through 78 Processing sheet with id= P, first strand: chain 'D' and resid 167 through 174 Processing sheet with id= Q, first strand: chain 'E' and resid 12 through 14 Processing sheet with id= R, first strand: chain 'E' and resid 145 through 148 removed outlier: 6.844A pdb=" N VAL E 16 " --> pdb=" O GLN E 146 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N TYR E 148 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE E 18 " --> pdb=" O TYR E 148 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP E 36 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE E 23 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LYS E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 76 through 78 Processing sheet with id= T, first strand: chain 'E' and resid 167 through 174 550 hydrogen bonds defined for protein. 1605 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: 3.98 Time building geometry restraints manager: 5.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2015 1.31 - 1.43: 3755 1.43 - 1.56: 7223 1.56 - 1.68: 77 1.68 - 1.81: 50 Bond restraints: 13120 Sorted by residual: bond pdb=" C34 LBN C 401 " pdb=" O7 LBN C 401 " ideal model delta sigma weight residual 1.331 1.427 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C34 LBN B 401 " pdb=" O7 LBN B 401 " ideal model delta sigma weight residual 1.331 1.426 -0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" C34 LBN E 401 " pdb=" O7 LBN E 401 " ideal model delta sigma weight residual 1.331 1.426 -0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" C34 LBN D 401 " pdb=" O7 LBN D 401 " ideal model delta sigma weight residual 1.331 1.426 -0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C34 LBN A 401 " pdb=" O7 LBN A 401 " ideal model delta sigma weight residual 1.331 1.426 -0.095 2.00e-02 2.50e+03 2.25e+01 ... (remaining 13115 not shown) Histogram of bond angle deviations from ideal: 98.83 - 105.87: 288 105.87 - 112.90: 6903 112.90 - 119.94: 4400 119.94 - 126.97: 6064 126.97 - 134.00: 175 Bond angle restraints: 17830 Sorted by residual: angle pdb=" N ASN C 60 " pdb=" CA ASN C 60 " pdb=" C ASN C 60 " ideal model delta sigma weight residual 111.07 119.92 -8.85 1.07e+00 8.73e-01 6.84e+01 angle pdb=" N ASN E 60 " pdb=" CA ASN E 60 " pdb=" C ASN E 60 " ideal model delta sigma weight residual 111.07 119.92 -8.85 1.07e+00 8.73e-01 6.84e+01 angle pdb=" N ASN A 60 " pdb=" CA ASN A 60 " pdb=" C ASN A 60 " ideal model delta sigma weight residual 111.07 119.91 -8.84 1.07e+00 8.73e-01 6.83e+01 angle pdb=" N ASN B 60 " pdb=" CA ASN B 60 " pdb=" C ASN B 60 " ideal model delta sigma weight residual 111.07 119.90 -8.83 1.07e+00 8.73e-01 6.80e+01 angle pdb=" N ASN D 60 " pdb=" CA ASN D 60 " pdb=" C ASN D 60 " ideal model delta sigma weight residual 111.07 119.87 -8.80 1.07e+00 8.73e-01 6.77e+01 ... (remaining 17825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.58: 7170 21.58 - 43.15: 435 43.15 - 64.73: 100 64.73 - 86.31: 25 86.31 - 107.88: 20 Dihedral angle restraints: 7750 sinusoidal: 3245 harmonic: 4505 Sorted by residual: dihedral pdb=" CA LEU B 118 " pdb=" C LEU B 118 " pdb=" N PHE B 119 " pdb=" CA PHE B 119 " ideal model delta harmonic sigma weight residual -180.00 -156.48 -23.52 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA LEU D 118 " pdb=" C LEU D 118 " pdb=" N PHE D 119 " pdb=" CA PHE D 119 " ideal model delta harmonic sigma weight residual -180.00 -156.48 -23.52 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA LEU A 118 " pdb=" C LEU A 118 " pdb=" N PHE A 119 " pdb=" CA PHE A 119 " ideal model delta harmonic sigma weight residual -180.00 -156.50 -23.50 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 7747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1518 0.064 - 0.129: 353 0.129 - 0.193: 53 0.193 - 0.257: 21 0.257 - 0.322: 10 Chirality restraints: 1955 Sorted by residual: chirality pdb=" CA GLU C 59 " pdb=" N GLU C 59 " pdb=" C GLU C 59 " pdb=" CB GLU C 59 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA GLU D 59 " pdb=" N GLU D 59 " pdb=" C GLU D 59 " pdb=" CB GLU D 59 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CA GLU A 59 " pdb=" N GLU A 59 " pdb=" C GLU A 59 " pdb=" CB GLU A 59 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 1952 not shown) Planarity restraints: 2250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 50 " 0.033 5.00e-02 4.00e+02 5.08e-02 4.12e+00 pdb=" N PRO D 51 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 51 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 51 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 50 " 0.033 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO A 51 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 51 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 51 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 50 " 0.033 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO B 51 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 51 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 51 " 0.028 5.00e-02 4.00e+02 ... (remaining 2247 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3431 2.81 - 3.33: 10736 3.33 - 3.86: 19954 3.86 - 4.38: 23616 4.38 - 4.90: 42828 Nonbonded interactions: 100565 Sorted by model distance: nonbonded pdb=" O TYR B 248 " pdb=" CD1 ILE B 252 " model vdw 2.290 3.460 nonbonded pdb=" O TYR D 248 " pdb=" CD1 ILE D 252 " model vdw 2.290 3.460 nonbonded pdb=" O TYR E 248 " pdb=" CD1 ILE E 252 " model vdw 2.291 3.460 nonbonded pdb=" O TYR C 248 " pdb=" CD1 ILE C 252 " model vdw 2.291 3.460 nonbonded pdb=" O TYR A 248 " pdb=" CD1 ILE A 252 " model vdw 2.291 3.460 ... (remaining 100560 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' selection = chain 'E' } 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: 0.240 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: 2.060 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 35.440 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.090 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 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 : 0.009 0.096 13120 Z= 0.574 Angle : 0.987 15.995 17830 Z= 0.540 Chirality : 0.062 0.322 1955 Planarity : 0.005 0.051 2250 Dihedral : 16.369 107.881 4840 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.98 % Favored : 94.69 % Rotamer: Outliers : 0.36 % Allowed : 1.45 % Favored : 98.18 % 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: -1.01 (0.21), residues: 1525 helix: -0.01 (0.21), residues: 530 sheet: 0.04 (0.25), residues: 490 loop : -1.99 (0.23), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 161 HIS 0.007 0.002 HIS C 177 PHE 0.024 0.003 PHE C 247 TYR 0.011 0.002 TYR A 204 ARG 0.005 0.001 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 160 time to evaluate : 1.381 Fit side-chains REVERT: A 163 ARG cc_start: 0.8147 (mmt-90) cc_final: 0.7737 (mmt-90) REVERT: A 245 TYR cc_start: 0.8383 (t80) cc_final: 0.8072 (t80) REVERT: C 61 THR cc_start: 0.8940 (m) cc_final: 0.8676 (p) REVERT: C 206 TRP cc_start: 0.7842 (m100) cc_final: 0.7614 (m100) REVERT: D 150 GLU cc_start: 0.7606 (pt0) cc_final: 0.7236 (pt0) REVERT: E 61 THR cc_start: 0.9014 (m) cc_final: 0.8737 (p) REVERT: E 150 GLU cc_start: 0.7678 (pt0) cc_final: 0.7462 (pt0) REVERT: E 174 ARG cc_start: 0.8206 (ttm-80) cc_final: 0.7964 (ttm170) REVERT: E 177 HIS cc_start: 0.6673 (p90) cc_final: 0.6049 (p90) outliers start: 5 outliers final: 0 residues processed: 161 average time/residue: 0.2943 time to fit residues: 65.8276 Evaluate side-chains 114 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 87 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 62 GLN A 151 ASN A 251 ASN B 60 ASN B 62 GLN B 251 ASN C 60 ASN C 62 GLN D 60 ASN D 62 GLN E 60 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13120 Z= 0.241 Angle : 0.516 6.149 17830 Z= 0.267 Chirality : 0.046 0.140 1955 Planarity : 0.004 0.036 2250 Dihedral : 14.185 112.277 1910 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.51 % Allowed : 4.73 % Favored : 94.76 % 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: -0.18 (0.22), residues: 1525 helix: 1.08 (0.22), residues: 535 sheet: 0.17 (0.25), residues: 500 loop : -1.72 (0.24), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 206 HIS 0.003 0.001 HIS E 177 PHE 0.021 0.002 PHE A 247 TYR 0.011 0.001 TYR E 245 ARG 0.002 0.000 ARG E 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 122 time to evaluate : 1.477 Fit side-chains REVERT: A 163 ARG cc_start: 0.8093 (mmt-90) cc_final: 0.7695 (mmt-90) REVERT: C 61 THR cc_start: 0.8970 (m) cc_final: 0.8348 (p) REVERT: D 150 GLU cc_start: 0.7631 (pt0) cc_final: 0.7306 (pt0) REVERT: E 174 ARG cc_start: 0.8174 (ttm-80) cc_final: 0.7919 (ttm170) outliers start: 7 outliers final: 3 residues processed: 127 average time/residue: 0.3043 time to fit residues: 53.9432 Evaluate side-chains 105 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 102 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain E residue 60 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 7.9990 chunk 42 optimal weight: 0.0020 chunk 113 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 136 optimal weight: 8.9990 chunk 147 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 109 optimal weight: 0.9990 overall best weight: 2.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 ASN D 251 ASN E 60 ASN E 251 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13120 Z= 0.330 Angle : 0.531 5.511 17830 Z= 0.274 Chirality : 0.047 0.144 1955 Planarity : 0.004 0.034 2250 Dihedral : 13.414 109.285 1910 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.51 % Allowed : 7.27 % Favored : 92.22 % 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: 0.10 (0.22), residues: 1525 helix: 1.47 (0.23), residues: 535 sheet: 0.17 (0.24), residues: 500 loop : -1.58 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 206 HIS 0.004 0.001 HIS E 177 PHE 0.019 0.002 PHE E 247 TYR 0.011 0.001 TYR E 245 ARG 0.002 0.000 ARG D 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 107 time to evaluate : 1.297 Fit side-chains REVERT: C 61 THR cc_start: 0.9029 (m) cc_final: 0.8430 (p) REVERT: D 150 GLU cc_start: 0.7671 (pt0) cc_final: 0.7389 (pt0) REVERT: E 174 ARG cc_start: 0.8173 (ttm-80) cc_final: 0.7955 (ttm170) outliers start: 7 outliers final: 5 residues processed: 111 average time/residue: 0.3278 time to fit residues: 49.9468 Evaluate side-chains 105 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 100 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 279 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 70 optimal weight: 0.0000 chunk 15 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 ASN C 251 ASN E 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13120 Z= 0.308 Angle : 0.512 5.452 17830 Z= 0.264 Chirality : 0.046 0.148 1955 Planarity : 0.004 0.033 2250 Dihedral : 12.371 107.254 1910 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.65 % Allowed : 7.93 % Favored : 91.42 % 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: 0.25 (0.22), residues: 1525 helix: 1.64 (0.23), residues: 535 sheet: 0.18 (0.24), residues: 500 loop : -1.48 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 206 HIS 0.004 0.001 HIS B 177 PHE 0.022 0.002 PHE D 247 TYR 0.011 0.001 TYR E 245 ARG 0.002 0.000 ARG A 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 109 time to evaluate : 1.516 Fit side-chains REVERT: C 61 THR cc_start: 0.8999 (m) cc_final: 0.8391 (p) REVERT: D 150 GLU cc_start: 0.7719 (pt0) cc_final: 0.7481 (pt0) REVERT: E 174 ARG cc_start: 0.8172 (ttm-80) cc_final: 0.7888 (ttm170) outliers start: 9 outliers final: 7 residues processed: 116 average time/residue: 0.3206 time to fit residues: 51.5426 Evaluate side-chains 107 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain E residue 60 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 59 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 130 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13120 Z= 0.153 Angle : 0.436 4.982 17830 Z= 0.224 Chirality : 0.044 0.131 1955 Planarity : 0.003 0.030 2250 Dihedral : 11.909 106.144 1910 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.87 % Allowed : 8.58 % Favored : 90.55 % 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 (0.22), residues: 1525 helix: 1.90 (0.24), residues: 535 sheet: 0.55 (0.24), residues: 490 loop : -1.32 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 43 HIS 0.002 0.000 HIS E 177 PHE 0.023 0.001 PHE D 247 TYR 0.010 0.001 TYR E 245 ARG 0.001 0.000 ARG E 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 118 time to evaluate : 1.423 Fit side-chains REVERT: A 150 GLU cc_start: 0.7781 (pt0) cc_final: 0.7450 (pt0) REVERT: D 60 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8373 (m-40) REVERT: E 174 ARG cc_start: 0.8171 (ttm-80) cc_final: 0.7879 (ttm170) outliers start: 12 outliers final: 9 residues processed: 128 average time/residue: 0.2984 time to fit residues: 53.3875 Evaluate side-chains 112 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 102 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 279 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 28 optimal weight: 0.2980 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 139 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 251 ASN E 60 ASN E 251 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13120 Z= 0.146 Angle : 0.424 4.944 17830 Z= 0.216 Chirality : 0.043 0.131 1955 Planarity : 0.003 0.028 2250 Dihedral : 11.129 104.196 1910 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.73 % Allowed : 9.16 % Favored : 90.11 % 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 (0.23), residues: 1525 helix: 2.03 (0.24), residues: 535 sheet: 0.58 (0.24), residues: 505 loop : -1.18 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 43 HIS 0.001 0.000 HIS D 284 PHE 0.019 0.001 PHE D 247 TYR 0.013 0.001 TYR A 248 ARG 0.001 0.000 ARG E 163 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 122 time to evaluate : 1.466 Fit side-chains REVERT: A 150 GLU cc_start: 0.7833 (pt0) cc_final: 0.7499 (pt0) REVERT: B 239 MET cc_start: 0.6730 (ttp) cc_final: 0.6367 (tpp) REVERT: B 245 TYR cc_start: 0.8078 (t80) cc_final: 0.7372 (t80) REVERT: B 279 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7385 (mm) REVERT: D 150 GLU cc_start: 0.7646 (pt0) cc_final: 0.7140 (mt-10) REVERT: E 163 ARG cc_start: 0.8002 (mmt-90) cc_final: 0.7702 (mmt180) REVERT: E 174 ARG cc_start: 0.8169 (ttm-80) cc_final: 0.7869 (ttm170) outliers start: 10 outliers final: 6 residues processed: 131 average time/residue: 0.3096 time to fit residues: 57.2800 Evaluate side-chains 121 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain E residue 279 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 122 optimal weight: 0.3980 chunk 81 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 89 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 13120 Z= 0.379 Angle : 0.533 5.580 17830 Z= 0.275 Chirality : 0.047 0.151 1955 Planarity : 0.004 0.034 2250 Dihedral : 11.230 100.910 1910 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.87 % Allowed : 9.67 % Favored : 89.45 % 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 (0.22), residues: 1525 helix: 1.91 (0.24), residues: 530 sheet: 0.46 (0.24), residues: 490 loop : -1.34 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 206 HIS 0.004 0.001 HIS B 177 PHE 0.033 0.002 PHE D 247 TYR 0.013 0.001 TYR D 248 ARG 0.002 0.000 ARG D 231 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 109 time to evaluate : 1.349 Fit side-chains REVERT: A 163 ARG cc_start: 0.7957 (mmt-90) cc_final: 0.7629 (mmp80) REVERT: A 245 TYR cc_start: 0.8215 (t80) cc_final: 0.7951 (t80) REVERT: C 61 THR cc_start: 0.8989 (m) cc_final: 0.8358 (p) REVERT: D 150 GLU cc_start: 0.7759 (pt0) cc_final: 0.7184 (mt-10) REVERT: E 174 ARG cc_start: 0.8142 (ttm-80) cc_final: 0.7822 (ttm170) outliers start: 12 outliers final: 10 residues processed: 120 average time/residue: 0.3273 time to fit residues: 54.9024 Evaluate side-chains 114 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 104 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 279 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 13 optimal weight: 0.4980 chunk 113 optimal weight: 0.8980 chunk 131 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 126 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 251 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13120 Z= 0.150 Angle : 0.430 4.980 17830 Z= 0.221 Chirality : 0.044 0.131 1955 Planarity : 0.003 0.028 2250 Dihedral : 10.460 101.411 1910 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.65 % Allowed : 10.18 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.23), residues: 1525 helix: 2.11 (0.24), residues: 530 sheet: 0.48 (0.24), residues: 500 loop : -1.09 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 43 HIS 0.002 0.001 HIS D 284 PHE 0.033 0.001 PHE A 247 TYR 0.014 0.001 TYR D 245 ARG 0.001 0.000 ARG D 231 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 109 time to evaluate : 1.398 Fit side-chains REVERT: A 150 GLU cc_start: 0.7801 (pt0) cc_final: 0.7454 (pt0) REVERT: B 245 TYR cc_start: 0.8079 (t80) cc_final: 0.7404 (t80) REVERT: D 150 GLU cc_start: 0.7703 (pt0) cc_final: 0.7159 (mt-10) REVERT: E 174 ARG cc_start: 0.8163 (ttm-80) cc_final: 0.7845 (ttm170) outliers start: 9 outliers final: 8 residues processed: 118 average time/residue: 0.3132 time to fit residues: 50.9989 Evaluate side-chains 113 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain E residue 279 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 58 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13120 Z= 0.326 Angle : 0.508 5.352 17830 Z= 0.261 Chirality : 0.046 0.148 1955 Planarity : 0.003 0.032 2250 Dihedral : 10.385 99.103 1910 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.80 % Allowed : 9.96 % Favored : 89.24 % 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 (0.22), residues: 1525 helix: 2.01 (0.24), residues: 530 sheet: 0.50 (0.24), residues: 490 loop : -1.27 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 206 HIS 0.004 0.001 HIS B 177 PHE 0.030 0.002 PHE D 247 TYR 0.015 0.001 TYR D 248 ARG 0.002 0.000 ARG E 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 103 time to evaluate : 1.436 Fit side-chains REVERT: A 163 ARG cc_start: 0.7959 (mmt-90) cc_final: 0.7630 (mmp80) REVERT: A 245 TYR cc_start: 0.8260 (t80) cc_final: 0.7972 (t80) REVERT: B 279 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7422 (mm) REVERT: C 61 THR cc_start: 0.8912 (m) cc_final: 0.8323 (p) REVERT: D 150 GLU cc_start: 0.7760 (pt0) cc_final: 0.7197 (mt-10) REVERT: E 174 ARG cc_start: 0.8141 (ttm-80) cc_final: 0.7817 (ttm170) outliers start: 11 outliers final: 10 residues processed: 112 average time/residue: 0.3241 time to fit residues: 50.8609 Evaluate side-chains 111 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain E residue 279 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 126 optimal weight: 0.7980 chunk 36 optimal weight: 0.3980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13120 Z= 0.149 Angle : 0.430 4.959 17830 Z= 0.221 Chirality : 0.044 0.133 1955 Planarity : 0.003 0.029 2250 Dihedral : 9.766 99.101 1910 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.80 % Allowed : 10.11 % Favored : 89.09 % 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 (0.23), residues: 1525 helix: 2.16 (0.24), residues: 530 sheet: 0.51 (0.24), residues: 500 loop : -1.05 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 43 HIS 0.002 0.001 HIS B 177 PHE 0.043 0.001 PHE D 247 TYR 0.014 0.001 TYR D 245 ARG 0.001 0.000 ARG E 163 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 113 time to evaluate : 1.425 Fit side-chains REVERT: A 150 GLU cc_start: 0.7833 (pt0) cc_final: 0.7487 (pt0) REVERT: B 245 TYR cc_start: 0.8031 (t80) cc_final: 0.7358 (t80) REVERT: B 279 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7513 (mm) REVERT: D 150 GLU cc_start: 0.7718 (pt0) cc_final: 0.7245 (mt-10) REVERT: E 163 ARG cc_start: 0.8005 (mmt-90) cc_final: 0.7712 (mmt180) REVERT: E 174 ARG cc_start: 0.8159 (ttm-80) cc_final: 0.7839 (ttm170) outliers start: 11 outliers final: 10 residues processed: 123 average time/residue: 0.3149 time to fit residues: 53.6839 Evaluate side-chains 120 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 109 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain E residue 279 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 6 optimal weight: 0.1980 chunk 86 optimal weight: 0.9980 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.147811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.099223 restraints weight = 13187.656| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.14 r_work: 0.2815 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13120 Z= 0.224 Angle : 0.465 5.102 17830 Z= 0.239 Chirality : 0.045 0.140 1955 Planarity : 0.003 0.030 2250 Dihedral : 9.557 96.233 1910 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.80 % Allowed : 10.18 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.23), residues: 1525 helix: 2.15 (0.24), residues: 530 sheet: 0.47 (0.24), residues: 500 loop : -1.09 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 206 HIS 0.003 0.001 HIS B 177 PHE 0.049 0.002 PHE A 247 TYR 0.013 0.001 TYR D 245 ARG 0.002 0.000 ARG B 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2595.12 seconds wall clock time: 47 minutes 43.80 seconds (2863.80 seconds total)