Starting phenix.real_space_refine on Thu Mar 14 21:17:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqh_33396/03_2024/7xqh_33396.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqh_33396/03_2024/7xqh_33396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqh_33396/03_2024/7xqh_33396.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqh_33396/03_2024/7xqh_33396.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqh_33396/03_2024/7xqh_33396.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqh_33396/03_2024/7xqh_33396.pdb" } resolution = 3.8 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= 0.001 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 48 5.16 5 C 6516 2.51 5 N 1548 2.21 5 O 1662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 42": "OE1" <-> "OE2" Residue "A GLU 48": "OE1" <-> "OE2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 101": "NH1" <-> "NH2" Residue "A GLU 112": "OE1" <-> "OE2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "B GLU 42": "OE1" <-> "OE2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B ARG 53": "NH1" <-> "NH2" Residue "B ARG 101": "NH1" <-> "NH2" Residue "B GLU 112": "OE1" <-> "OE2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "C GLU 48": "OE1" <-> "OE2" Residue "C ARG 53": "NH1" <-> "NH2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C GLU 112": "OE1" <-> "OE2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D GLU 48": "OE1" <-> "OE2" Residue "D ARG 53": "NH1" <-> "NH2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D GLU 112": "OE1" <-> "OE2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E GLU 48": "OE1" <-> "OE2" Residue "E ARG 53": "NH1" <-> "NH2" Residue "E ARG 101": "NH1" <-> "NH2" Residue "E GLU 112": "OE1" <-> "OE2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E GLU 166": "OE1" <-> "OE2" Residue "F GLU 42": "OE1" <-> "OE2" Residue "F GLU 48": "OE1" <-> "OE2" Residue "F ARG 53": "NH1" <-> "NH2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F GLU 112": "OE1" <-> "OE2" Residue "F ARG 148": "NH1" <-> "NH2" Residue "F GLU 166": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9774 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1629 Classifications: {'peptide': 200} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 193} Chain breaks: 1 Chain: "B" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1629 Classifications: {'peptide': 200} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 193} Chain breaks: 1 Chain: "C" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1629 Classifications: {'peptide': 200} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 193} Chain breaks: 1 Chain: "D" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1629 Classifications: {'peptide': 200} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 193} Chain breaks: 1 Chain: "E" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1629 Classifications: {'peptide': 200} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 193} Chain breaks: 1 Chain: "F" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1629 Classifications: {'peptide': 200} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 193} Chain breaks: 1 Time building chain proxies: 5.50, per 1000 atoms: 0.56 Number of scatterers: 9774 At special positions: 0 Unit cell: (102.608, 106, 102.608, 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 48 16.00 O 1662 8.00 N 1548 7.00 C 6516 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 187 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 192 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 187 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 192 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 187 " 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: 3.59 Conformation dependent library (CDL) restraints added in 1.6 seconds 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2268 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 6 sheets defined 72.0% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 20 through 25 Processing helix chain 'A' and resid 27 through 32 Processing helix chain 'A' and resid 33 through 40 Processing helix chain 'A' and resid 40 through 45 removed outlier: 3.801A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TRP A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 40 through 45' Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.972A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 107 removed outlier: 3.535A pdb=" N VAL A 87 " --> pdb=" O ILE A 83 " (cutoff:3.500A) Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 149 through 177 removed outlier: 4.059A pdb=" N ARG A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 235 removed outlier: 3.848A pdb=" N LYS A 206 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 228 " --> pdb=" O ASN A 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 20 through 25 Processing helix chain 'B' and resid 27 through 32 Processing helix chain 'B' and resid 33 through 40 Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.800A pdb=" N ALA B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TRP B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 40 through 45' Processing helix chain 'B' and resid 60 through 70 removed outlier: 3.972A pdb=" N VAL B 64 " --> pdb=" O GLY B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 107 removed outlier: 3.535A pdb=" N VAL B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 149 through 177 removed outlier: 4.058A pdb=" N ARG B 153 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 235 removed outlier: 3.848A pdb=" N LYS B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 228 " --> pdb=" O ASN B 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 15 Processing helix chain 'C' and resid 20 through 25 Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 33 through 40 Processing helix chain 'C' and resid 40 through 45 removed outlier: 3.801A pdb=" N ALA C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TRP C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 40 through 45' Processing helix chain 'C' and resid 60 through 70 removed outlier: 3.972A pdb=" N VAL C 64 " --> pdb=" O GLY C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 107 removed outlier: 3.535A pdb=" N VAL C 87 " --> pdb=" O ILE C 83 " (cutoff:3.500A) Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 149 through 177 removed outlier: 4.059A pdb=" N ARG C 153 " --> pdb=" O GLY C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 235 removed outlier: 3.848A pdb=" N LYS C 206 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU C 228 " --> pdb=" O ASN C 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 15 Processing helix chain 'D' and resid 20 through 25 Processing helix chain 'D' and resid 27 through 32 Processing helix chain 'D' and resid 33 through 40 Processing helix chain 'D' and resid 40 through 45 removed outlier: 3.801A pdb=" N ALA D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TRP D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 40 through 45' Processing helix chain 'D' and resid 60 through 70 removed outlier: 3.972A pdb=" N VAL D 64 " --> pdb=" O GLY D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 107 removed outlier: 3.535A pdb=" N VAL D 87 " --> pdb=" O ILE D 83 " (cutoff:3.500A) Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 149 through 177 removed outlier: 4.059A pdb=" N ARG D 153 " --> pdb=" O GLY D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 235 removed outlier: 3.848A pdb=" N LYS D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU D 227 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU D 228 " --> pdb=" O ASN D 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 15 Processing helix chain 'E' and resid 20 through 25 Processing helix chain 'E' and resid 27 through 32 Processing helix chain 'E' and resid 33 through 40 Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.801A pdb=" N ALA E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TRP E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 40 through 45' Processing helix chain 'E' and resid 60 through 70 removed outlier: 3.972A pdb=" N VAL E 64 " --> pdb=" O GLY E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 107 removed outlier: 3.535A pdb=" N VAL E 87 " --> pdb=" O ILE E 83 " (cutoff:3.500A) Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 149 through 177 removed outlier: 4.059A pdb=" N ARG E 153 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 235 removed outlier: 3.848A pdb=" N LYS E 206 " --> pdb=" O ARG E 202 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU E 227 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU E 228 " --> pdb=" O ASN E 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 15 Processing helix chain 'F' and resid 20 through 25 Processing helix chain 'F' and resid 27 through 32 Processing helix chain 'F' and resid 33 through 40 Processing helix chain 'F' and resid 40 through 45 removed outlier: 3.801A pdb=" N ALA F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TRP F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 40 through 45' Processing helix chain 'F' and resid 60 through 70 removed outlier: 3.972A pdb=" N VAL F 64 " --> pdb=" O GLY F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 107 removed outlier: 3.535A pdb=" N VAL F 87 " --> pdb=" O ILE F 83 " (cutoff:3.500A) Proline residue: F 88 - end of helix Processing helix chain 'F' and resid 149 through 177 removed outlier: 4.059A pdb=" N ARG F 153 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 235 removed outlier: 3.848A pdb=" N LYS F 206 " --> pdb=" O ARG F 202 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU F 227 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU F 228 " --> pdb=" O ASN F 224 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.623A pdb=" N ARG A 53 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.623A pdb=" N ARG B 53 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.623A pdb=" N ARG C 53 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.623A pdb=" N ARG D 53 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.623A pdb=" N ARG E 53 " --> pdb=" O PHE E 199 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.623A pdb=" N ARG F 53 " --> pdb=" O PHE F 199 " (cutoff:3.500A) 612 hydrogen bonds defined for protein. 1818 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.35 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2898 1.34 - 1.46: 2154 1.46 - 1.57: 4920 1.57 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 10032 Sorted by residual: bond pdb=" CA VAL B 87 " pdb=" C VAL B 87 " ideal model delta sigma weight residual 1.520 1.538 -0.018 8.80e-03 1.29e+04 4.35e+00 bond pdb=" CA VAL E 87 " pdb=" C VAL E 87 " ideal model delta sigma weight residual 1.520 1.538 -0.018 8.80e-03 1.29e+04 4.28e+00 bond pdb=" CA VAL F 87 " pdb=" C VAL F 87 " ideal model delta sigma weight residual 1.520 1.538 -0.018 8.80e-03 1.29e+04 4.25e+00 bond pdb=" CA VAL C 87 " pdb=" C VAL C 87 " ideal model delta sigma weight residual 1.520 1.538 -0.018 8.80e-03 1.29e+04 4.25e+00 bond pdb=" CA VAL A 87 " pdb=" C VAL A 87 " ideal model delta sigma weight residual 1.520 1.538 -0.018 8.80e-03 1.29e+04 4.20e+00 ... (remaining 10027 not shown) Histogram of bond angle deviations from ideal: 100.39 - 107.11: 192 107.11 - 113.82: 5671 113.82 - 120.54: 4230 120.54 - 127.26: 3395 127.26 - 133.98: 102 Bond angle restraints: 13590 Sorted by residual: angle pdb=" C SER D 86 " pdb=" N VAL D 87 " pdb=" CA VAL D 87 " ideal model delta sigma weight residual 120.24 124.52 -4.28 6.30e-01 2.52e+00 4.63e+01 angle pdb=" C SER B 86 " pdb=" N VAL B 87 " pdb=" CA VAL B 87 " ideal model delta sigma weight residual 120.24 124.52 -4.28 6.30e-01 2.52e+00 4.62e+01 angle pdb=" C SER A 86 " pdb=" N VAL A 87 " pdb=" CA VAL A 87 " ideal model delta sigma weight residual 120.24 124.51 -4.27 6.30e-01 2.52e+00 4.60e+01 angle pdb=" C SER C 86 " pdb=" N VAL C 87 " pdb=" CA VAL C 87 " ideal model delta sigma weight residual 120.24 124.51 -4.27 6.30e-01 2.52e+00 4.60e+01 angle pdb=" C SER F 86 " pdb=" N VAL F 87 " pdb=" CA VAL F 87 " ideal model delta sigma weight residual 120.24 124.50 -4.26 6.30e-01 2.52e+00 4.58e+01 ... (remaining 13585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.78: 4992 13.78 - 27.56: 534 27.56 - 41.33: 222 41.33 - 55.11: 90 55.11 - 68.89: 36 Dihedral angle restraints: 5874 sinusoidal: 2364 harmonic: 3510 Sorted by residual: dihedral pdb=" CA TYR E 177 " pdb=" C TYR E 177 " pdb=" N GLY E 178 " pdb=" CA GLY E 178 " ideal model delta harmonic sigma weight residual -180.00 -163.31 -16.69 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA TYR A 177 " pdb=" C TYR A 177 " pdb=" N GLY A 178 " pdb=" CA GLY A 178 " ideal model delta harmonic sigma weight residual 180.00 -163.34 -16.66 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA TYR B 177 " pdb=" C TYR B 177 " pdb=" N GLY B 178 " pdb=" CA GLY B 178 " ideal model delta harmonic sigma weight residual 180.00 -163.35 -16.65 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 5871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1119 0.044 - 0.088: 334 0.088 - 0.132: 83 0.132 - 0.176: 0 0.176 - 0.220: 6 Chirality restraints: 1542 Sorted by residual: chirality pdb=" CA HIS A 194 " pdb=" N HIS A 194 " pdb=" C HIS A 194 " pdb=" CB HIS A 194 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA HIS D 194 " pdb=" N HIS D 194 " pdb=" C HIS D 194 " pdb=" CB HIS D 194 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA HIS E 194 " pdb=" N HIS E 194 " pdb=" C HIS E 194 " pdb=" CB HIS E 194 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1539 not shown) Planarity restraints: 1644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 87 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.48e+00 pdb=" N PRO B 88 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 88 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 88 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 87 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.48e+00 pdb=" N PRO E 88 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO E 88 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 88 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 87 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO C 88 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 88 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 88 " 0.027 5.00e-02 4.00e+02 ... (remaining 1641 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 3398 2.85 - 3.36: 8833 3.36 - 3.87: 15659 3.87 - 4.39: 15479 4.39 - 4.90: 27451 Nonbonded interactions: 70820 Sorted by model distance: nonbonded pdb=" O LEU C 35 " pdb=" OG1 THR C 39 " model vdw 2.337 2.440 nonbonded pdb=" O LEU B 35 " pdb=" OG1 THR B 39 " model vdw 2.337 2.440 nonbonded pdb=" O LEU E 35 " pdb=" OG1 THR E 39 " model vdw 2.338 2.440 nonbonded pdb=" O LEU A 35 " pdb=" OG1 THR A 39 " model vdw 2.338 2.440 nonbonded pdb=" O LEU D 35 " pdb=" OG1 THR D 39 " model vdw 2.338 2.440 ... (remaining 70815 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' selection = chain 'F' } 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 group one per residue 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.940 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 26.310 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 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 0.053 10032 Z= 0.298 Angle : 0.781 7.929 13590 Z= 0.475 Chirality : 0.042 0.220 1542 Planarity : 0.006 0.047 1644 Dihedral : 15.527 68.889 3552 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.57 % Favored : 95.92 % Rotamer: Outliers : 2.23 % Allowed : 15.08 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.21), residues: 1176 helix: -1.31 (0.15), residues: 774 sheet: 2.72 (0.64), residues: 66 loop : -1.88 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 78 HIS 0.001 0.000 HIS D 95 PHE 0.011 0.001 PHE D 52 TYR 0.010 0.002 TYR F 92 ARG 0.003 0.001 ARG F 202 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 227 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8384 (p0) cc_final: 0.8140 (p0) REVERT: A 100 MET cc_start: 0.8239 (ttt) cc_final: 0.7884 (ttt) REVERT: A 104 GLU cc_start: 0.9259 (tt0) cc_final: 0.9014 (pt0) REVERT: A 190 ASP cc_start: 0.8872 (m-30) cc_final: 0.8635 (t0) REVERT: B 212 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.8340 (t80) REVERT: C 47 ASP cc_start: 0.8435 (p0) cc_final: 0.8195 (p0) REVERT: C 100 MET cc_start: 0.8139 (ttt) cc_final: 0.7810 (ttt) REVERT: C 104 GLU cc_start: 0.9281 (tt0) cc_final: 0.9011 (pt0) REVERT: C 190 ASP cc_start: 0.8807 (m-30) cc_final: 0.8514 (t0) REVERT: D 47 ASP cc_start: 0.8393 (p0) cc_final: 0.8178 (p0) REVERT: D 100 MET cc_start: 0.8246 (ttt) cc_final: 0.7944 (ttt) REVERT: D 104 GLU cc_start: 0.9301 (tt0) cc_final: 0.9029 (pt0) REVERT: D 190 ASP cc_start: 0.8852 (m-30) cc_final: 0.8558 (t0) REVERT: E 100 MET cc_start: 0.8083 (ttt) cc_final: 0.7604 (tmm) REVERT: E 104 GLU cc_start: 0.9378 (tt0) cc_final: 0.8962 (pt0) REVERT: E 212 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.8288 (t80) REVERT: F 47 ASP cc_start: 0.8452 (p0) cc_final: 0.8201 (p0) REVERT: F 100 MET cc_start: 0.8186 (ttt) cc_final: 0.7883 (ttt) REVERT: F 104 GLU cc_start: 0.9277 (tt0) cc_final: 0.9015 (pt0) REVERT: F 190 ASP cc_start: 0.8832 (m-30) cc_final: 0.8526 (t0) outliers start: 24 outliers final: 22 residues processed: 239 average time/residue: 0.1874 time to fit residues: 64.4511 Evaluate side-chains 184 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 160 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 229 PHE Chi-restraints excluded: chain D residue 3 ASP Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain F residue 3 ASP Chi-restraints excluded: chain F residue 197 ASP Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain F residue 229 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 61 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 224 ASN B 63 ASN B 81 GLN B 224 ASN C 81 GLN C 224 ASN D 81 GLN D 224 ASN E 81 GLN E 224 ASN F 81 GLN F 224 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10032 Z= 0.189 Angle : 0.617 9.540 13590 Z= 0.309 Chirality : 0.039 0.186 1542 Planarity : 0.003 0.021 1644 Dihedral : 7.391 59.707 1338 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.51 % Allowed : 2.55 % Favored : 96.94 % Rotamer: Outliers : 8.94 % Allowed : 15.08 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.58 (0.24), residues: 1176 helix: 0.95 (0.17), residues: 780 sheet: 3.83 (0.68), residues: 60 loop : -1.58 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 4 HIS 0.002 0.001 HIS D 194 PHE 0.007 0.001 PHE E 179 TYR 0.008 0.001 TYR E 92 ARG 0.002 0.000 ARG C 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 153 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8347 (ttt) cc_final: 0.8017 (ttt) REVERT: A 104 GLU cc_start: 0.9356 (tt0) cc_final: 0.9039 (pt0) REVERT: A 190 ASP cc_start: 0.8888 (m-30) cc_final: 0.8679 (t0) REVERT: A 223 LEU cc_start: 0.9389 (tp) cc_final: 0.9059 (tt) REVERT: B 104 GLU cc_start: 0.8782 (pt0) cc_final: 0.8320 (mm-30) REVERT: C 47 ASP cc_start: 0.8388 (p0) cc_final: 0.8106 (p0) REVERT: C 100 MET cc_start: 0.8308 (ttt) cc_final: 0.7989 (ttt) REVERT: C 104 GLU cc_start: 0.9330 (tt0) cc_final: 0.9057 (pt0) REVERT: C 190 ASP cc_start: 0.8792 (m-30) cc_final: 0.8553 (t0) REVERT: D 47 ASP cc_start: 0.8385 (p0) cc_final: 0.8156 (p0) REVERT: D 100 MET cc_start: 0.8361 (ttt) cc_final: 0.8061 (ttt) REVERT: D 104 GLU cc_start: 0.9371 (tt0) cc_final: 0.9037 (pt0) REVERT: D 190 ASP cc_start: 0.8884 (m-30) cc_final: 0.8650 (t0) REVERT: D 223 LEU cc_start: 0.9421 (tp) cc_final: 0.9095 (tt) REVERT: E 100 MET cc_start: 0.8234 (ttt) cc_final: 0.7900 (ttp) REVERT: E 104 GLU cc_start: 0.9460 (tt0) cc_final: 0.9221 (pt0) REVERT: E 213 MET cc_start: 0.8888 (mmp) cc_final: 0.8472 (mmp) REVERT: F 47 ASP cc_start: 0.8399 (p0) cc_final: 0.8121 (p0) REVERT: F 100 MET cc_start: 0.8330 (ttt) cc_final: 0.8000 (ttt) REVERT: F 104 GLU cc_start: 0.9326 (tt0) cc_final: 0.9054 (pt0) REVERT: F 190 ASP cc_start: 0.8798 (m-30) cc_final: 0.8549 (t0) outliers start: 96 outliers final: 64 residues processed: 216 average time/residue: 0.1863 time to fit residues: 58.3893 Evaluate side-chains 197 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 133 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 229 PHE Chi-restraints excluded: chain D residue 3 ASP Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain F residue 3 ASP Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 197 ASP Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain F residue 224 ASN Chi-restraints excluded: chain F residue 229 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 20.0000 chunk 33 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 chunk 74 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10032 Z= 0.207 Angle : 0.630 10.294 13590 Z= 0.307 Chirality : 0.039 0.214 1542 Planarity : 0.003 0.024 1644 Dihedral : 7.003 59.980 1332 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.51 % Allowed : 2.98 % Favored : 96.51 % Rotamer: Outliers : 7.91 % Allowed : 16.85 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.36 (0.25), residues: 1176 helix: 1.47 (0.18), residues: 816 sheet: 3.65 (0.71), residues: 60 loop : -1.27 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 4 HIS 0.003 0.001 HIS B 74 PHE 0.009 0.001 PHE F 52 TYR 0.012 0.001 TYR B 177 ARG 0.001 0.000 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 144 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8378 (p0) cc_final: 0.8171 (p0) REVERT: A 100 MET cc_start: 0.8376 (ttt) cc_final: 0.8025 (ttt) REVERT: A 104 GLU cc_start: 0.9367 (tt0) cc_final: 0.9054 (pt0) REVERT: B 91 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8869 (tt) REVERT: B 103 GLU cc_start: 0.9544 (mm-30) cc_final: 0.9067 (mm-30) REVERT: B 104 GLU cc_start: 0.8777 (pt0) cc_final: 0.8359 (mm-30) REVERT: C 47 ASP cc_start: 0.8397 (p0) cc_final: 0.7691 (p0) REVERT: C 100 MET cc_start: 0.8356 (ttt) cc_final: 0.8004 (ttt) REVERT: C 104 GLU cc_start: 0.9364 (tt0) cc_final: 0.9078 (pt0) REVERT: C 190 ASP cc_start: 0.8774 (m-30) cc_final: 0.8551 (t0) REVERT: C 202 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7731 (mtm180) REVERT: C 223 LEU cc_start: 0.9457 (tp) cc_final: 0.9170 (tt) REVERT: D 47 ASP cc_start: 0.8387 (p0) cc_final: 0.8183 (p0) REVERT: D 100 MET cc_start: 0.8355 (ttt) cc_final: 0.8037 (ttt) REVERT: D 104 GLU cc_start: 0.9388 (tt0) cc_final: 0.9054 (pt0) REVERT: D 190 ASP cc_start: 0.8853 (m-30) cc_final: 0.8631 (t0) REVERT: D 223 LEU cc_start: 0.9399 (tp) cc_final: 0.9123 (tt) REVERT: E 100 MET cc_start: 0.8295 (ttt) cc_final: 0.7937 (ttp) REVERT: E 104 GLU cc_start: 0.9472 (tt0) cc_final: 0.9203 (pt0) REVERT: E 213 MET cc_start: 0.8946 (mmp) cc_final: 0.8470 (mmp) REVERT: E 223 LEU cc_start: 0.9497 (tp) cc_final: 0.9229 (tt) REVERT: F 47 ASP cc_start: 0.8410 (p0) cc_final: 0.8142 (p0) REVERT: F 190 ASP cc_start: 0.8785 (m-30) cc_final: 0.8554 (t0) REVERT: F 223 LEU cc_start: 0.9453 (tp) cc_final: 0.9165 (tt) outliers start: 85 outliers final: 64 residues processed: 197 average time/residue: 0.2033 time to fit residues: 56.3007 Evaluate side-chains 202 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 136 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 3 ASP Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain F residue 3 ASP Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 3.9990 chunk 82 optimal weight: 0.0980 chunk 56 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 73 optimal weight: 0.5980 chunk 109 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10032 Z= 0.179 Angle : 0.589 10.507 13590 Z= 0.286 Chirality : 0.038 0.183 1542 Planarity : 0.003 0.024 1644 Dihedral : 5.929 59.858 1314 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.51 % Allowed : 2.47 % Favored : 97.02 % Rotamer: Outliers : 6.24 % Allowed : 19.18 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.96 (0.26), residues: 1176 helix: 1.98 (0.19), residues: 816 sheet: 3.25 (0.72), residues: 60 loop : -1.07 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 4 HIS 0.003 0.001 HIS B 74 PHE 0.007 0.001 PHE F 52 TYR 0.012 0.001 TYR C 66 ARG 0.001 0.000 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 135 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8399 (p0) cc_final: 0.8190 (p0) REVERT: B 91 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8871 (tt) REVERT: B 104 GLU cc_start: 0.8843 (pt0) cc_final: 0.8451 (tp30) REVERT: B 212 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.8226 (t80) REVERT: C 190 ASP cc_start: 0.8737 (m-30) cc_final: 0.8537 (t0) REVERT: D 47 ASP cc_start: 0.8381 (p0) cc_final: 0.8161 (p0) REVERT: D 190 ASP cc_start: 0.8823 (m-30) cc_final: 0.8605 (t0) REVERT: D 223 LEU cc_start: 0.9369 (tp) cc_final: 0.9080 (tt) REVERT: E 100 MET cc_start: 0.8340 (ttt) cc_final: 0.8073 (ttt) REVERT: E 104 GLU cc_start: 0.9474 (tt0) cc_final: 0.9241 (pt0) REVERT: E 213 MET cc_start: 0.8968 (mmp) cc_final: 0.8448 (mmp) REVERT: F 47 ASP cc_start: 0.8382 (p0) cc_final: 0.7685 (p0) REVERT: F 190 ASP cc_start: 0.8749 (m-30) cc_final: 0.8521 (t0) REVERT: F 202 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7630 (mtm180) outliers start: 67 outliers final: 58 residues processed: 178 average time/residue: 0.1823 time to fit residues: 46.6391 Evaluate side-chains 184 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 123 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 1 optimal weight: 20.0000 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 80 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 59 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 63 ASN C 49 GLN F 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10032 Z= 0.168 Angle : 0.593 11.724 13590 Z= 0.282 Chirality : 0.038 0.155 1542 Planarity : 0.003 0.024 1644 Dihedral : 5.692 59.970 1302 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.51 % Allowed : 2.64 % Favored : 96.85 % Rotamer: Outliers : 6.52 % Allowed : 20.39 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.26), residues: 1176 helix: 2.20 (0.19), residues: 816 sheet: 2.64 (0.74), residues: 60 loop : -1.08 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 78 HIS 0.003 0.001 HIS F 74 PHE 0.007 0.001 PHE C 52 TYR 0.014 0.001 TYR D 66 ARG 0.005 0.000 ARG B 53 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 128 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8860 (tt) REVERT: B 104 GLU cc_start: 0.8822 (pt0) cc_final: 0.8438 (tp30) REVERT: B 212 PHE cc_start: 0.9146 (OUTLIER) cc_final: 0.8252 (t80) REVERT: B 223 LEU cc_start: 0.9433 (tp) cc_final: 0.9174 (tt) REVERT: D 190 ASP cc_start: 0.8800 (m-30) cc_final: 0.8596 (t0) REVERT: D 223 LEU cc_start: 0.9364 (tp) cc_final: 0.9084 (tt) REVERT: E 100 MET cc_start: 0.8353 (ttt) cc_final: 0.8101 (ttt) REVERT: E 104 GLU cc_start: 0.9487 (tt0) cc_final: 0.9246 (pt0) REVERT: F 190 ASP cc_start: 0.8688 (m-30) cc_final: 0.8484 (t0) REVERT: F 202 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7405 (mtm180) outliers start: 70 outliers final: 57 residues processed: 175 average time/residue: 0.1911 time to fit residues: 48.4432 Evaluate side-chains 180 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 120 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 68 optimal weight: 0.0470 chunk 28 optimal weight: 0.9990 chunk 116 optimal weight: 0.5980 chunk 96 optimal weight: 0.4980 chunk 53 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN F 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10032 Z= 0.131 Angle : 0.578 10.507 13590 Z= 0.270 Chirality : 0.037 0.151 1542 Planarity : 0.003 0.025 1644 Dihedral : 5.535 59.911 1302 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.51 % Allowed : 2.04 % Favored : 97.45 % Rotamer: Outliers : 5.59 % Allowed : 21.04 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.26), residues: 1176 helix: 2.44 (0.19), residues: 810 sheet: 2.32 (0.75), residues: 60 loop : -1.23 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 78 HIS 0.002 0.001 HIS B 74 PHE 0.006 0.001 PHE E 169 TYR 0.008 0.001 TYR D 66 ARG 0.004 0.000 ARG B 53 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 149 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 TYR cc_start: 0.8619 (t80) cc_final: 0.8306 (t80) REVERT: A 223 LEU cc_start: 0.9376 (tp) cc_final: 0.9017 (tt) REVERT: B 91 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8861 (tt) REVERT: B 104 GLU cc_start: 0.8791 (pt0) cc_final: 0.8430 (tp30) REVERT: B 212 PHE cc_start: 0.9094 (OUTLIER) cc_final: 0.8192 (t80) REVERT: C 92 TYR cc_start: 0.8663 (t80) cc_final: 0.8333 (t80) REVERT: D 92 TYR cc_start: 0.8594 (t80) cc_final: 0.8276 (t80) REVERT: D 190 ASP cc_start: 0.8738 (m-30) cc_final: 0.8536 (t0) REVERT: D 223 LEU cc_start: 0.9337 (tp) cc_final: 0.9063 (tt) REVERT: E 100 MET cc_start: 0.8345 (ttt) cc_final: 0.8059 (ttt) REVERT: E 104 GLU cc_start: 0.9484 (tt0) cc_final: 0.9220 (pt0) REVERT: E 212 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.8169 (t80) REVERT: F 49 GLN cc_start: 0.9511 (OUTLIER) cc_final: 0.9305 (tp40) REVERT: F 92 TYR cc_start: 0.8667 (t80) cc_final: 0.8268 (t80) outliers start: 60 outliers final: 47 residues processed: 188 average time/residue: 0.1585 time to fit residues: 45.3318 Evaluate side-chains 189 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 138 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 49 GLN Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 8.9990 chunk 13 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10032 Z= 0.132 Angle : 0.596 12.638 13590 Z= 0.273 Chirality : 0.037 0.152 1542 Planarity : 0.002 0.027 1644 Dihedral : 5.513 59.995 1302 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.51 % Allowed : 2.21 % Favored : 97.28 % Rotamer: Outliers : 4.66 % Allowed : 22.91 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.26), residues: 1176 helix: 2.34 (0.19), residues: 828 sheet: 2.28 (0.77), residues: 60 loop : -1.36 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP F 78 HIS 0.002 0.001 HIS F 74 PHE 0.006 0.001 PHE E 169 TYR 0.012 0.001 TYR B 17 ARG 0.001 0.000 ARG B 53 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 143 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.9370 (tp) cc_final: 0.9103 (tt) REVERT: B 91 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8883 (tt) REVERT: B 104 GLU cc_start: 0.8818 (pt0) cc_final: 0.8443 (tp30) REVERT: B 212 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8183 (t80) REVERT: D 223 LEU cc_start: 0.9334 (tp) cc_final: 0.9068 (tt) REVERT: E 100 MET cc_start: 0.8336 (ttt) cc_final: 0.8049 (ttt) REVERT: E 104 GLU cc_start: 0.9490 (tt0) cc_final: 0.9209 (pt0) REVERT: E 212 PHE cc_start: 0.9018 (OUTLIER) cc_final: 0.8176 (t80) outliers start: 50 outliers final: 43 residues processed: 176 average time/residue: 0.1635 time to fit residues: 43.9080 Evaluate side-chains 184 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 138 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 105 optimal weight: 0.0770 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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: 0.8248 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10032 Z= 0.130 Angle : 0.594 12.349 13590 Z= 0.273 Chirality : 0.037 0.152 1542 Planarity : 0.003 0.028 1644 Dihedral : 5.489 59.942 1302 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.51 % Allowed : 1.79 % Favored : 97.70 % Rotamer: Outliers : 4.84 % Allowed : 24.02 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.26), residues: 1176 helix: 2.41 (0.19), residues: 828 sheet: 2.24 (0.76), residues: 60 loop : -1.42 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP F 78 HIS 0.002 0.001 HIS F 74 PHE 0.006 0.001 PHE E 169 TYR 0.019 0.001 TYR B 92 ARG 0.005 0.000 ARG B 53 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 150 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 TYR cc_start: 0.8520 (t80) cc_final: 0.8281 (t80) REVERT: A 223 LEU cc_start: 0.9387 (tp) cc_final: 0.9051 (tt) REVERT: B 91 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8867 (tt) REVERT: B 104 GLU cc_start: 0.8817 (pt0) cc_final: 0.8462 (tp30) REVERT: B 212 PHE cc_start: 0.9091 (OUTLIER) cc_final: 0.8194 (t80) REVERT: C 92 TYR cc_start: 0.8477 (t80) cc_final: 0.8271 (t80) REVERT: D 223 LEU cc_start: 0.9332 (tp) cc_final: 0.9072 (tt) REVERT: E 91 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8764 (tt) REVERT: E 100 MET cc_start: 0.8313 (ttt) cc_final: 0.8020 (ttt) REVERT: E 104 GLU cc_start: 0.9505 (tt0) cc_final: 0.9199 (pt0) REVERT: E 212 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.8152 (t80) outliers start: 52 outliers final: 42 residues processed: 185 average time/residue: 0.1684 time to fit residues: 47.4589 Evaluate side-chains 190 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 144 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 95 HIS Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 7.9990 chunk 101 optimal weight: 20.0000 chunk 107 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 84 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 70 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 GLN F 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10032 Z= 0.151 Angle : 0.603 12.192 13590 Z= 0.277 Chirality : 0.037 0.149 1542 Planarity : 0.003 0.028 1644 Dihedral : 5.516 59.845 1302 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.51 % Allowed : 2.47 % Favored : 97.02 % Rotamer: Outliers : 4.93 % Allowed : 24.67 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.26), residues: 1176 helix: 2.44 (0.19), residues: 828 sheet: 2.15 (0.77), residues: 60 loop : -1.43 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 78 HIS 0.003 0.001 HIS A 74 PHE 0.007 0.001 PHE E 169 TYR 0.022 0.001 TYR F 92 ARG 0.005 0.000 ARG B 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 141 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8413 (p0) cc_final: 0.8205 (p0) REVERT: A 92 TYR cc_start: 0.8553 (t80) cc_final: 0.8297 (t80) REVERT: A 223 LEU cc_start: 0.9389 (tp) cc_final: 0.9051 (tt) REVERT: B 29 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8791 (tt) REVERT: B 91 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8861 (tt) REVERT: B 104 GLU cc_start: 0.8808 (pt0) cc_final: 0.8450 (tp30) REVERT: B 212 PHE cc_start: 0.9141 (OUTLIER) cc_final: 0.8231 (t80) REVERT: C 92 TYR cc_start: 0.8477 (t80) cc_final: 0.8248 (t80) REVERT: D 49 GLN cc_start: 0.9453 (OUTLIER) cc_final: 0.9006 (mm110) REVERT: D 223 LEU cc_start: 0.9334 (tp) cc_final: 0.9072 (tt) REVERT: E 91 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8796 (tt) REVERT: E 100 MET cc_start: 0.8348 (ttt) cc_final: 0.8039 (ttt) REVERT: E 104 GLU cc_start: 0.9499 (tt0) cc_final: 0.9193 (pt0) REVERT: E 212 PHE cc_start: 0.9045 (OUTLIER) cc_final: 0.8176 (t80) outliers start: 53 outliers final: 43 residues processed: 178 average time/residue: 0.1629 time to fit residues: 44.2171 Evaluate side-chains 188 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 139 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 95 HIS Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN D 49 GLN D 224 ASN F 224 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10032 Z= 0.215 Angle : 0.624 11.898 13590 Z= 0.295 Chirality : 0.038 0.146 1542 Planarity : 0.003 0.028 1644 Dihedral : 5.619 59.749 1302 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.83 % Favored : 95.66 % Rotamer: Outliers : 5.03 % Allowed : 24.49 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.26), residues: 1176 helix: 2.82 (0.18), residues: 798 sheet: 1.95 (0.78), residues: 60 loop : -1.53 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 4 HIS 0.002 0.001 HIS F 74 PHE 0.010 0.001 PHE D 52 TYR 0.025 0.001 TYR F 92 ARG 0.005 0.000 ARG B 53 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 129 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8819 (tt) REVERT: A 47 ASP cc_start: 0.8446 (p0) cc_final: 0.8237 (p0) REVERT: A 92 TYR cc_start: 0.8633 (t80) cc_final: 0.8253 (t80) REVERT: B 29 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8817 (tt) REVERT: B 91 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8858 (tt) REVERT: B 104 GLU cc_start: 0.8805 (pt0) cc_final: 0.8459 (tp30) REVERT: B 212 PHE cc_start: 0.9186 (OUTLIER) cc_final: 0.8250 (t80) REVERT: C 92 TYR cc_start: 0.8563 (t80) cc_final: 0.8178 (t80) REVERT: E 91 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8798 (tt) REVERT: E 100 MET cc_start: 0.8318 (ttt) cc_final: 0.7987 (ttt) REVERT: E 104 GLU cc_start: 0.9498 (tt0) cc_final: 0.9196 (pt0) REVERT: E 212 PHE cc_start: 0.9102 (OUTLIER) cc_final: 0.8209 (t80) outliers start: 54 outliers final: 46 residues processed: 171 average time/residue: 0.1611 time to fit residues: 42.1583 Evaluate side-chains 183 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 131 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 95 HIS Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 95 HIS Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain F residue 224 ASN Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 224 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.093273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.070389 restraints weight = 30638.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.072625 restraints weight = 14711.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.074047 restraints weight = 9301.736| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 10032 Z= 0.221 Angle : 0.896 59.200 13590 Z= 0.517 Chirality : 0.040 0.554 1542 Planarity : 0.003 0.067 1644 Dihedral : 5.730 59.741 1302 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.60 % Allowed : 3.74 % Favored : 95.66 % Rotamer: Outliers : 4.84 % Allowed : 25.23 % Favored : 69.93 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 16.67 % 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: 2.53 (0.26), residues: 1176 helix: 2.80 (0.19), residues: 798 sheet: 1.95 (0.78), residues: 60 loop : -1.52 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 78 HIS 0.003 0.001 HIS A 74 PHE 0.010 0.001 PHE D 52 TYR 0.023 0.001 TYR F 92 ARG 0.004 0.000 ARG B 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1790.44 seconds wall clock time: 33 minutes 16.37 seconds (1996.37 seconds total)