Starting phenix.real_space_refine on Wed Feb 14 06:39:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8f_31017/02_2024/7e8f_31017.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8f_31017/02_2024/7e8f_31017.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8f_31017/02_2024/7e8f_31017.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8f_31017/02_2024/7e8f_31017.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8f_31017/02_2024/7e8f_31017.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8f_31017/02_2024/7e8f_31017.pdb" } resolution = 3.18 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= 0.001 sd= 0.009 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 37 5.16 5 C 5569 2.51 5 N 1468 2.21 5 O 1694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 40": "OD1" <-> "OD2" Residue "A ASP 80": "OD1" <-> "OD2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A ASP 287": "OD1" <-> "OD2" Residue "H ASP 113": "OD1" <-> "OD2" Residue "C GLU 6": "OE1" <-> "OE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C ASP 73": "OD1" <-> "OD2" Residue "B ARG 82": "NH1" <-> "NH2" Residue "B ASP 87": "OD1" <-> "OD2" Residue "B TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D ASP 89": "OD1" <-> "OD2" Residue "R PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 408": "NH1" <-> "NH2" Residue "R ASP 427": "OD1" <-> "OD2" Residue "R PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 465": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8768 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2079 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 243} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "H" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 938 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "L" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 780 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "C" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 944 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "B" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 852 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "D" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 874 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "E" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "R" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1498 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 9, 'TRANS': 179} Chain breaks: 1 Time building chain proxies: 5.11, per 1000 atoms: 0.58 Number of scatterers: 8768 At special positions: 0 Unit cell: (133.604, 78.9, 99.94, 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 37 16.00 O 1694 8.00 N 1468 7.00 C 5569 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 93 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.06 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.04 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.03 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: 3.22 Conformation dependent library (CDL) restraints added in 1.9 seconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2052 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 26 sheets defined 5.7% alpha, 42.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'H' and resid 27 through 32 removed outlier: 3.546A pdb=" N SER H 30 " --> pdb=" O PHE H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 103 through 108 removed outlier: 4.672A pdb=" N SER H 108 " --> pdb=" O SER H 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 30 removed outlier: 3.582A pdb=" N ASP L 29 " --> pdb=" O LYS L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.900A pdb=" N GLU L 82 " --> pdb=" O ALA L 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.783A pdb=" N THR D 90 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 52 No H-bonds generated for 'chain 'E' and resid 50 through 52' Processing helix chain 'R' and resid 365 through 370 removed outlier: 3.797A pdb=" N ASN R 370 " --> pdb=" O SER R 366 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 410 removed outlier: 4.567A pdb=" N ARG R 408 " --> pdb=" O ASP R 405 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'R' and resid 438 through 443 removed outlier: 3.526A pdb=" N SER R 443 " --> pdb=" O ASN R 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.458A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.392A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.004A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 154 through 160 removed outlier: 9.840A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 11.101A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 10.282A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.113A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 9.241A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ARG A 246 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 160 removed outlier: 9.840A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 11.101A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 10.282A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.113A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 9.241A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ARG A 246 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.664A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.039A pdb=" N VAL H 114 " --> pdb=" O THR H 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.838A pdb=" N VAL L 10 " --> pdb=" O THR L 104 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA L 83 " --> pdb=" O LEU L 103 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLN L 36 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LEU L 45 " --> pdb=" O GLN L 36 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.838A pdb=" N VAL L 10 " --> pdb=" O THR L 104 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA L 83 " --> pdb=" O LEU L 103 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AB3, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.587A pdb=" N SER C 21 " --> pdb=" O SER C 7 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 11 through 12 removed outlier: 5.871A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ALA C 40 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU C 45 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.807A pdb=" N CYS C 96 " --> pdb=" O TRP C 115 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TRP C 115 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS C 98 " --> pdb=" O ASP C 113 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AB7, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.514A pdb=" N GLU B 110 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU B 38 " --> pdb=" O TYR B 54 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N TYR B 54 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP B 40 " --> pdb=" O LEU B 52 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB9, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AC1, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.496A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N MET D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TYR D 33 " --> pdb=" O ASP D 98 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL D 106 " --> pdb=" O ARG D 97 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU D 99 " --> pdb=" O MET D 104 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N MET D 104 " --> pdb=" O LEU D 99 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.496A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N MET D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TYR D 33 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 5 through 7 Processing sheet with id=AC4, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.578A pdb=" N LEU E 11 " --> pdb=" O LYS E 103 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'R' and resid 354 through 358 removed outlier: 3.515A pdb=" N LYS R 378 " --> pdb=" O VAL R 433 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'R' and resid 361 through 362 removed outlier: 6.707A pdb=" N CYS R 361 " --> pdb=" O CYS R 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'R' and resid 473 through 474 326 hydrogen bonds defined for protein. 801 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: 3.32 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2807 1.35 - 1.48: 2512 1.48 - 1.61: 3611 1.61 - 1.74: 0 1.74 - 1.87: 49 Bond restraints: 8979 Sorted by residual: bond pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " ideal model delta sigma weight residual 1.808 1.873 -0.065 3.30e-02 9.18e+02 3.84e+00 bond pdb=" CA CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sigma weight residual 1.536 1.500 0.036 2.08e-02 2.31e+03 3.03e+00 bond pdb=" CB PRO L 8 " pdb=" CG PRO L 8 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.01e+00 bond pdb=" C GLN B 47 " pdb=" N SER B 48 " ideal model delta sigma weight residual 1.340 1.258 0.082 5.87e-02 2.90e+02 1.95e+00 bond pdb=" CG LEU R 461 " pdb=" CD1 LEU R 461 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.86e+00 ... (remaining 8974 not shown) Histogram of bond angle deviations from ideal: 99.52 - 106.43: 233 106.43 - 113.34: 4711 113.34 - 120.26: 3127 120.26 - 127.17: 4035 127.17 - 134.08: 91 Bond angle restraints: 12197 Sorted by residual: angle pdb=" CA CYS R 432 " pdb=" CB CYS R 432 " pdb=" SG CYS R 432 " ideal model delta sigma weight residual 114.40 125.49 -11.09 2.30e+00 1.89e-01 2.32e+01 angle pdb=" CA PRO L 8 " pdb=" N PRO L 8 " pdb=" CD PRO L 8 " ideal model delta sigma weight residual 112.00 105.50 6.50 1.40e+00 5.10e-01 2.16e+01 angle pdb=" CA CYS A 166 " pdb=" CB CYS A 166 " pdb=" SG CYS A 166 " ideal model delta sigma weight residual 114.40 124.20 -9.80 2.30e+00 1.89e-01 1.82e+01 angle pdb=" C ILE E 29 " pdb=" N SER E 30 " pdb=" CA SER E 30 " ideal model delta sigma weight residual 121.54 128.44 -6.90 1.91e+00 2.74e-01 1.31e+01 angle pdb=" N SER E 30 " pdb=" CA SER E 30 " pdb=" C SER E 30 " ideal model delta sigma weight residual 110.80 118.40 -7.60 2.13e+00 2.20e-01 1.27e+01 ... (remaining 12192 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.09: 4761 18.09 - 36.19: 418 36.19 - 54.28: 64 54.28 - 72.38: 9 72.38 - 90.47: 7 Dihedral angle restraints: 5259 sinusoidal: 2015 harmonic: 3244 Sorted by residual: dihedral pdb=" CA HIS B 31 " pdb=" C HIS B 31 " pdb=" N SER B 32 " pdb=" CA SER B 32 " ideal model delta harmonic sigma weight residual 180.00 143.72 36.28 0 5.00e+00 4.00e-02 5.27e+01 dihedral pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " pdb=" SG CYS R 432 " pdb=" CB CYS R 432 " ideal model delta sinusoidal sigma weight residual 93.00 42.44 50.56 1 1.00e+01 1.00e-02 3.50e+01 dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual 93.00 45.01 47.99 1 1.00e+01 1.00e-02 3.17e+01 ... (remaining 5256 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 958 0.045 - 0.089: 273 0.089 - 0.134: 92 0.134 - 0.178: 3 0.178 - 0.223: 3 Chirality restraints: 1329 Sorted by residual: chirality pdb=" CA CYS A 166 " pdb=" N CYS A 166 " pdb=" C CYS A 166 " pdb=" CB CYS A 166 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA CYS R 432 " pdb=" N CYS R 432 " pdb=" C CYS R 432 " pdb=" CB CYS R 432 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA THR B 99 " pdb=" N THR B 99 " pdb=" C THR B 99 " pdb=" CB THR B 99 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 8.03e-01 ... (remaining 1326 not shown) Planarity restraints: 1569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO L 7 " -0.085 5.00e-02 4.00e+02 1.26e-01 2.54e+01 pdb=" N PRO L 8 " 0.218 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 14 " -0.046 5.00e-02 4.00e+02 6.92e-02 7.65e+00 pdb=" N PRO B 15 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 15 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 15 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 347 " 0.017 2.00e-02 2.50e+03 1.72e-02 5.15e+00 pdb=" CG PHE R 347 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE R 347 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE R 347 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE R 347 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE R 347 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE R 347 " 0.001 2.00e-02 2.50e+03 ... (remaining 1566 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 313 2.71 - 3.25: 8172 3.25 - 3.80: 13819 3.80 - 4.35: 18791 4.35 - 4.90: 31839 Nonbonded interactions: 72934 Sorted by model distance: nonbonded pdb=" OH TYR C 107 " pdb=" OG SER B 32 " model vdw 2.157 2.440 nonbonded pdb=" OG SER E 30 " pdb=" OE1 GLN R 498 " model vdw 2.170 2.440 nonbonded pdb=" OE1 GLN L 36 " pdb=" OH TYR L 85 " model vdw 2.186 2.440 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.205 2.440 nonbonded pdb=" OH TYR A 144 " pdb=" OE2 GLU A 156 " model vdw 2.207 2.440 ... (remaining 72929 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.310 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 27.530 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 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 0.087 8979 Z= 0.334 Angle : 0.682 11.089 12197 Z= 0.377 Chirality : 0.046 0.223 1329 Planarity : 0.005 0.126 1569 Dihedral : 13.858 90.470 3171 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.64 (0.24), residues: 1112 helix: -4.20 (0.58), residues: 27 sheet: -0.58 (0.25), residues: 419 loop : -1.30 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 47 HIS 0.005 0.001 HIS B 31 PHE 0.039 0.002 PHE R 347 TYR 0.014 0.002 TYR R 505 ARG 0.009 0.001 ARG R 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.105 Fit side-chains REVERT: H 56 SER cc_start: 0.8477 (p) cc_final: 0.8251 (p) REVERT: D 19 ARG cc_start: 0.7236 (ttp-170) cc_final: 0.6939 (ttp-170) REVERT: D 61 ASP cc_start: 0.7102 (m-30) cc_final: 0.6892 (p0) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2298 time to fit residues: 50.5618 Evaluate side-chains 142 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 28 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.0815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 8979 Z= 0.271 Angle : 0.644 12.454 12197 Z= 0.342 Chirality : 0.046 0.207 1329 Planarity : 0.005 0.080 1569 Dihedral : 5.620 36.107 1241 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 0.52 % Allowed : 7.64 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.38 (0.25), residues: 1112 helix: -4.36 (0.47), residues: 32 sheet: -0.26 (0.25), residues: 447 loop : -1.20 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 47 HIS 0.005 0.001 HIS A 207 PHE 0.028 0.002 PHE A 79 TYR 0.012 0.001 TYR A 265 ARG 0.006 0.001 ARG R 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 154 time to evaluate : 0.914 Fit side-chains REVERT: D 19 ARG cc_start: 0.7191 (ttp-170) cc_final: 0.6931 (ttp-170) REVERT: D 61 ASP cc_start: 0.7117 (m-30) cc_final: 0.6912 (p0) REVERT: R 444 LYS cc_start: 0.8278 (ttmt) cc_final: 0.7989 (ttmt) outliers start: 5 outliers final: 3 residues processed: 157 average time/residue: 0.2049 time to fit residues: 44.1304 Evaluate side-chains 144 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 141 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain C residue 69 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 67 optimal weight: 0.0980 chunk 27 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 98 optimal weight: 0.0980 chunk 33 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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: 0.7773 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8979 Z= 0.217 Angle : 0.583 9.953 12197 Z= 0.310 Chirality : 0.044 0.219 1329 Planarity : 0.004 0.066 1569 Dihedral : 5.259 34.490 1241 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.67 % Allowed : 10.25 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.11 (0.25), residues: 1112 helix: -4.33 (0.48), residues: 32 sheet: -0.11 (0.25), residues: 451 loop : -0.99 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 47 HIS 0.004 0.001 HIS A 207 PHE 0.022 0.001 PHE A 79 TYR 0.013 0.001 TYR A 265 ARG 0.005 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 162 time to evaluate : 0.970 Fit side-chains REVERT: D 61 ASP cc_start: 0.7196 (m-30) cc_final: 0.6949 (p0) REVERT: R 444 LYS cc_start: 0.8295 (ttmt) cc_final: 0.7948 (ttmt) outliers start: 16 outliers final: 10 residues processed: 174 average time/residue: 0.2273 time to fit residues: 53.1418 Evaluate side-chains 160 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 150 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain R residue 382 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 9.9990 chunk 74 optimal weight: 0.0870 chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 99 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 8979 Z= 0.359 Angle : 0.674 13.145 12197 Z= 0.356 Chirality : 0.047 0.269 1329 Planarity : 0.005 0.062 1569 Dihedral : 5.624 36.785 1241 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 2.20 % Allowed : 12.55 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.25), residues: 1112 helix: -4.33 (0.47), residues: 32 sheet: -0.13 (0.25), residues: 449 loop : -1.06 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 47 HIS 0.005 0.001 HIS A 207 PHE 0.028 0.002 PHE A 79 TYR 0.014 0.002 TYR B 37 ARG 0.006 0.001 ARG R 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 149 time to evaluate : 1.009 Fit side-chains REVERT: H 56 SER cc_start: 0.8479 (p) cc_final: 0.8260 (p) REVERT: D 61 ASP cc_start: 0.7191 (m-30) cc_final: 0.6955 (p0) REVERT: R 444 LYS cc_start: 0.8216 (ttmt) cc_final: 0.7864 (ttmt) outliers start: 21 outliers final: 15 residues processed: 162 average time/residue: 0.2227 time to fit residues: 50.0030 Evaluate side-chains 159 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 144 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain R residue 382 VAL Chi-restraints excluded: chain R residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 89 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 94 optimal weight: 0.8980 chunk 26 optimal weight: 0.0570 chunk 35 optimal weight: 0.6980 overall best weight: 1.9100 ------------------------------------------------------------------------------- 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: 0.7778 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8979 Z= 0.221 Angle : 0.594 11.235 12197 Z= 0.314 Chirality : 0.044 0.234 1329 Planarity : 0.004 0.058 1569 Dihedral : 5.290 34.575 1241 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 1.88 % Allowed : 13.18 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.06 (0.25), residues: 1112 helix: -4.28 (0.48), residues: 32 sheet: -0.09 (0.24), residues: 455 loop : -0.95 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 47 HIS 0.005 0.001 HIS B 31 PHE 0.018 0.001 PHE H 29 TYR 0.012 0.001 TYR A 265 ARG 0.007 0.000 ARG R 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 154 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: D 61 ASP cc_start: 0.7220 (m-30) cc_final: 0.6981 (p0) REVERT: E 31 SER cc_start: 0.7768 (m) cc_final: 0.7382 (p) REVERT: R 444 LYS cc_start: 0.8321 (ttmt) cc_final: 0.7965 (ttmt) outliers start: 18 outliers final: 9 residues processed: 166 average time/residue: 0.2175 time to fit residues: 49.0466 Evaluate side-chains 159 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 150 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 95 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 chunk 105 optimal weight: 6.9990 chunk 87 optimal weight: 20.0000 chunk 48 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 101 optimal weight: 0.3980 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8979 Z= 0.243 Angle : 0.604 12.285 12197 Z= 0.319 Chirality : 0.045 0.275 1329 Planarity : 0.004 0.036 1569 Dihedral : 5.271 35.101 1241 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 2.30 % Allowed : 13.91 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.00 (0.25), residues: 1112 helix: -4.29 (0.47), residues: 32 sheet: -0.01 (0.25), residues: 444 loop : -0.93 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 47 HIS 0.006 0.001 HIS A 207 PHE 0.020 0.002 PHE H 29 TYR 0.011 0.001 TYR A 265 ARG 0.007 0.000 ARG R 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 149 time to evaluate : 1.048 Fit side-chains revert: symmetry clash REVERT: A 40 ASP cc_start: 0.6618 (OUTLIER) cc_final: 0.6152 (p0) REVERT: C 73 ASP cc_start: 0.7876 (t0) cc_final: 0.7671 (t0) REVERT: C 76 LYS cc_start: 0.8116 (mtpt) cc_final: 0.7882 (mtmt) REVERT: D 61 ASP cc_start: 0.7243 (m-30) cc_final: 0.7009 (p0) REVERT: E 31 SER cc_start: 0.7777 (m) cc_final: 0.7369 (p) REVERT: R 444 LYS cc_start: 0.8292 (ttmt) cc_final: 0.7930 (ttmt) outliers start: 22 outliers final: 17 residues processed: 164 average time/residue: 0.2113 time to fit residues: 47.8950 Evaluate side-chains 165 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 147 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain R residue 382 VAL Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 7.9990 chunk 60 optimal weight: 0.3980 chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 41 optimal weight: 0.0470 overall best weight: 1.8482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8979 Z= 0.212 Angle : 0.583 12.630 12197 Z= 0.308 Chirality : 0.044 0.280 1329 Planarity : 0.004 0.034 1569 Dihedral : 5.147 34.064 1241 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.51 % Allowed : 13.70 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.96 (0.25), residues: 1112 helix: -4.26 (0.48), residues: 32 sheet: 0.01 (0.25), residues: 444 loop : -0.89 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 47 HIS 0.006 0.001 HIS A 207 PHE 0.018 0.001 PHE H 29 TYR 0.012 0.001 TYR A 265 ARG 0.006 0.000 ARG R 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 152 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: C 76 LYS cc_start: 0.8142 (mtpt) cc_final: 0.7833 (mtmt) REVERT: D 61 ASP cc_start: 0.7254 (m-30) cc_final: 0.7021 (p0) REVERT: E 31 SER cc_start: 0.7515 (m) cc_final: 0.7157 (p) REVERT: R 444 LYS cc_start: 0.8295 (ttmt) cc_final: 0.7918 (ttmt) outliers start: 24 outliers final: 15 residues processed: 168 average time/residue: 0.2075 time to fit residues: 47.9516 Evaluate side-chains 163 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 148 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain R residue 503 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 82 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 8979 Z= 0.315 Angle : 0.641 13.736 12197 Z= 0.338 Chirality : 0.046 0.307 1329 Planarity : 0.004 0.036 1569 Dihedral : 5.450 35.752 1241 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 2.72 % Allowed : 14.12 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.04 (0.25), residues: 1112 helix: -4.28 (0.49), residues: 32 sheet: -0.04 (0.25), residues: 455 loop : -0.96 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 47 HIS 0.009 0.002 HIS A 207 PHE 0.023 0.002 PHE H 29 TYR 0.013 0.002 TYR B 37 ARG 0.006 0.001 ARG R 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 150 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: C 76 LYS cc_start: 0.8223 (mtpt) cc_final: 0.7963 (mtpt) REVERT: D 61 ASP cc_start: 0.7229 (m-30) cc_final: 0.6996 (p0) REVERT: E 31 SER cc_start: 0.7584 (m) cc_final: 0.7232 (p) REVERT: R 444 LYS cc_start: 0.8179 (ttmt) cc_final: 0.7836 (ttmt) outliers start: 26 outliers final: 20 residues processed: 168 average time/residue: 0.2152 time to fit residues: 49.8645 Evaluate side-chains 167 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 147 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain R residue 347 PHE Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 503 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 0.0970 chunk 76 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8979 Z= 0.212 Angle : 0.593 13.700 12197 Z= 0.313 Chirality : 0.045 0.296 1329 Planarity : 0.004 0.034 1569 Dihedral : 5.222 34.330 1241 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.20 % Allowed : 14.96 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.25), residues: 1112 helix: -4.23 (0.50), residues: 32 sheet: 0.09 (0.25), residues: 443 loop : -0.93 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 47 HIS 0.004 0.001 HIS B 31 PHE 0.018 0.001 PHE H 29 TYR 0.012 0.001 TYR A 265 ARG 0.008 0.000 ARG R 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 147 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: D 61 ASP cc_start: 0.7253 (m-30) cc_final: 0.7014 (p0) REVERT: R 444 LYS cc_start: 0.8289 (ttmt) cc_final: 0.7920 (ttmt) outliers start: 21 outliers final: 18 residues processed: 162 average time/residue: 0.2110 time to fit residues: 47.2324 Evaluate side-chains 165 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 147 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain R residue 347 PHE Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 432 CYS Chi-restraints excluded: chain R residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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: 0.7782 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8979 Z= 0.271 Angle : 0.621 13.888 12197 Z= 0.327 Chirality : 0.045 0.312 1329 Planarity : 0.004 0.035 1569 Dihedral : 5.342 35.303 1241 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 2.20 % Allowed : 14.75 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.25), residues: 1112 helix: -4.26 (0.50), residues: 32 sheet: 0.09 (0.25), residues: 438 loop : -0.98 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 47 HIS 0.004 0.001 HIS B 31 PHE 0.021 0.002 PHE H 29 TYR 0.012 0.002 TYR B 37 ARG 0.006 0.000 ARG R 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 146 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: B 112 LYS cc_start: 0.7445 (ttmm) cc_final: 0.6978 (ttmt) REVERT: D 61 ASP cc_start: 0.7263 (m-30) cc_final: 0.7029 (p0) REVERT: R 444 LYS cc_start: 0.8292 (ttmt) cc_final: 0.7949 (ttmt) outliers start: 21 outliers final: 21 residues processed: 160 average time/residue: 0.2093 time to fit residues: 46.4194 Evaluate side-chains 167 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 146 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain R residue 347 PHE Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 432 CYS Chi-restraints excluded: chain R residue 503 VAL Chi-restraints excluded: chain R residue 516 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.3247 r_free = 0.3247 target = 0.117966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.098758 restraints weight = 10655.623| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.54 r_work: 0.2876 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8979 Z= 0.236 Angle : 0.601 13.740 12197 Z= 0.316 Chirality : 0.045 0.296 1329 Planarity : 0.004 0.035 1569 Dihedral : 5.263 34.430 1241 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.51 % Allowed : 14.75 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.96 (0.25), residues: 1112 helix: -4.24 (0.50), residues: 32 sheet: 0.11 (0.25), residues: 438 loop : -0.97 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 47 HIS 0.004 0.001 HIS B 31 PHE 0.019 0.002 PHE H 29 TYR 0.011 0.001 TYR A 265 ARG 0.007 0.000 ARG R 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2074.71 seconds wall clock time: 38 minutes 29.90 seconds (2309.90 seconds total)