Starting phenix.real_space_refine on Fri Apr 5 19:50:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vyf_43659/04_2024/8vyf_43659.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vyf_43659/04_2024/8vyf_43659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vyf_43659/04_2024/8vyf_43659.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vyf_43659/04_2024/8vyf_43659.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vyf_43659/04_2024/8vyf_43659.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vyf_43659/04_2024/8vyf_43659.pdb" } resolution = 3.2 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= 0.078 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 19 5.16 5 C 3245 2.51 5 N 868 2.21 5 O 1000 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 34": "NH1" <-> "NH2" Residue "A ARG 44": "NH1" <-> "NH2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 38": "NH1" <-> "NH2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B ARG 72": "NH1" <-> "NH2" Residue "B ARG 87": "NH1" <-> "NH2" Residue "B TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 103": "NH1" <-> "NH2" Residue "B ASP 110": "OD1" <-> "OD2" Residue "C ARG 18": "NH1" <-> "NH2" Residue "C ARG 30": "NH1" <-> "NH2" Residue "C TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 61": "NH1" <-> "NH2" Residue "C PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 5132 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2088 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 14, 'TRANS': 250} Chain breaks: 3 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 936 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 785 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "H" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 628 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 7, 'TRANS': 111} Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 402 Unresolved non-hydrogen dihedrals: 249 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 3, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 143 Chain: "L" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 530 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 7, 'TRANS': 97} Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 355 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 158 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 3.57, per 1000 atoms: 0.70 Number of scatterers: 5132 At special positions: 0 Unit cell: (85.143, 113.805, 76.713, 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 19 16.00 O 1000 8.00 N 868 7.00 C 3245 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 284 " - pdb=" SG CYS A 294 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.02 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1301 " - " ASN A 275 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 149 " " NAG A1304 " - " ASN A 17 " " NAG A1305 " - " ASN A 246 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 234 " " NAG F 1 " - " ASN A 61 " Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 1.2 seconds 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1318 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 11 sheets defined 5.3% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'L' and resid 26 through 30 Processing helix chain 'L' and resid 78 through 82 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.925A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N ASN A 61 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N TYR A 262 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ALA A 257 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR A 95 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.330A pdb=" N THR A 267 " --> pdb=" O ASP A 283 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ASP A 283 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU A 269 " --> pdb=" O ALA A 281 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA A 281 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LYS A 271 " --> pdb=" O THR A 279 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 84 through 85 current: chain 'A' and resid 116 through 121 removed outlier: 3.595A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 9.663A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.080A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 152 through 172 current: chain 'A' and resid 250 through 252 Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 10 through 12 current: chain 'B' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 58 through 60 current: chain 'B' and resid 111 through 112 Processing sheet with id=AA6, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 10 through 12 current: chain 'C' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 53 through 54 current: chain 'C' and resid 97 through 98 Processing sheet with id=AA8, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AA9, first strand: chain 'H' and resid 35 through 41 removed outlier: 6.184A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 59 through 61 current: chain 'H' and resid 109 through 115 Processing sheet with id=AB1, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.560A pdb=" N VAL L 10 " --> pdb=" O THR L 104 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLN L 36 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N LEU L 45 " --> pdb=" O GLN L 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 18 through 23 154 hydrogen bonds defined for protein. 369 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.25 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1113 1.33 - 1.45: 1243 1.45 - 1.58: 2868 1.58 - 1.70: 2 1.70 - 1.83: 24 Bond restraints: 5250 Sorted by residual: bond pdb=" CB LEU A 176 " pdb=" CG LEU A 176 " ideal model delta sigma weight residual 1.530 1.586 -0.056 2.00e-02 2.50e+03 7.83e+00 bond pdb=" C5 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.413 1.468 -0.055 2.00e-02 2.50e+03 7.64e+00 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.468 -0.055 2.00e-02 2.50e+03 7.54e+00 bond pdb=" C5 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.413 1.468 -0.055 2.00e-02 2.50e+03 7.52e+00 bond pdb=" C5 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.413 1.468 -0.055 2.00e-02 2.50e+03 7.46e+00 ... (remaining 5245 not shown) Histogram of bond angle deviations from ideal: 101.43 - 107.94: 213 107.94 - 114.45: 2901 114.45 - 120.97: 2420 120.97 - 127.48: 1620 127.48 - 133.99: 33 Bond angle restraints: 7187 Sorted by residual: angle pdb=" C GLN L 6 " pdb=" N PRO L 7 " pdb=" CA PRO L 7 " ideal model delta sigma weight residual 119.66 126.36 -6.70 7.30e-01 1.88e+00 8.42e+01 angle pdb=" C GLN H 41 " pdb=" N PRO H 42 " pdb=" CA PRO H 42 " ideal model delta sigma weight residual 119.66 126.07 -6.41 7.30e-01 1.88e+00 7.70e+01 angle pdb=" C LEU A 24 " pdb=" N PRO A 25 " pdb=" CA PRO A 25 " ideal model delta sigma weight residual 119.66 125.40 -5.74 7.30e-01 1.88e+00 6.17e+01 angle pdb=" C PRO A 25 " pdb=" N PRO A 26 " pdb=" CA PRO A 26 " ideal model delta sigma weight residual 119.85 127.34 -7.49 1.01e+00 9.80e-01 5.49e+01 angle pdb=" C ASP A 138 " pdb=" N PRO A 139 " pdb=" CA PRO A 139 " ideal model delta sigma weight residual 119.85 127.21 -7.36 1.01e+00 9.80e-01 5.31e+01 ... (remaining 7182 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.47: 3138 21.47 - 42.94: 50 42.94 - 64.41: 13 64.41 - 85.88: 7 85.88 - 107.35: 6 Dihedral angle restraints: 3214 sinusoidal: 1159 harmonic: 2055 Sorted by residual: dihedral pdb=" CB CYS L 22 " pdb=" SG CYS L 22 " pdb=" SG CYS L 87 " pdb=" CB CYS L 87 " ideal model delta sinusoidal sigma weight residual 93.00 47.21 45.79 1 1.00e+01 1.00e-02 2.91e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 50.51 42.49 1 1.00e+01 1.00e-02 2.52e+01 dihedral pdb=" O4 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.64 107.35 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 3211 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 601 0.065 - 0.129: 174 0.129 - 0.193: 43 0.193 - 0.258: 18 0.258 - 0.322: 11 Chirality restraints: 847 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 4.62e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 3.10e+01 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.49 0.09 2.00e-02 2.50e+03 1.98e+01 ... (remaining 844 not shown) Planarity restraints: 942 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 165 " -0.025 2.00e-02 2.50e+03 2.59e-02 8.42e+00 pdb=" CG ASN A 165 " 0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN A 165 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 165 " 0.039 2.00e-02 2.50e+03 pdb=" C1 NAG A1302 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 122 " 0.017 2.00e-02 2.50e+03 1.79e-02 4.01e+00 pdb=" CG ASN A 122 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN A 122 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN A 122 " -0.027 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 144 " -0.026 2.00e-02 2.50e+03 1.38e-02 3.79e+00 pdb=" CG TYR A 144 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR A 144 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 144 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 144 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 144 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 144 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 144 " -0.020 2.00e-02 2.50e+03 ... (remaining 939 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 2706 3.00 - 3.47: 4222 3.47 - 3.95: 7930 3.95 - 4.42: 8833 4.42 - 4.90: 14919 Nonbonded interactions: 38610 Sorted by model distance: nonbonded pdb=" ND1 HIS A 146 " pdb=" N LYS A 147 " model vdw 2.519 3.200 nonbonded pdb=" OD1 ASP A 80 " pdb=" N ASN A 81 " model vdw 2.554 2.520 nonbonded pdb=" OG SER A 172 " pdb=" N GLN A 173 " model vdw 2.616 2.520 nonbonded pdb=" N GLY B 33 " pdb=" O GLY B 33 " model vdw 2.618 2.496 nonbonded pdb=" OD2 ASP C 92 " pdb=" ND2 ASN C 93 " model vdw 2.627 2.520 ... (remaining 38605 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 '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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.710 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: 0.000 Extract box with map and model: 27.680 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 18.680 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 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 : 0.010 0.058 5250 Z= 0.689 Angle : 1.274 8.084 7187 Z= 0.855 Chirality : 0.077 0.322 847 Planarity : 0.005 0.019 934 Dihedral : 11.195 107.348 1875 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 0.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.25 (0.32), residues: 699 helix: 0.78 (1.60), residues: 11 sheet: 1.21 (0.30), residues: 300 loop : 0.64 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP B 47 HIS 0.005 0.001 HIS A 69 PHE 0.015 0.003 PHE A 55 TYR 0.026 0.004 TYR A 144 ARG 0.003 0.000 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.921 Fit side-chains REVERT: A 41 LYS cc_start: 0.7842 (mttt) cc_final: 0.7271 (mmtt) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.2216 time to fit residues: 30.0511 Evaluate side-chains 66 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 0.7980 chunk 52 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 188 ASN B 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5250 Z= 0.232 Angle : 0.566 7.153 7187 Z= 0.294 Chirality : 0.045 0.183 847 Planarity : 0.004 0.029 934 Dihedral : 7.280 64.792 1004 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.12 % Allowed : 6.13 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.33 (0.33), residues: 699 helix: 1.74 (1.52), residues: 11 sheet: 1.22 (0.30), residues: 307 loop : 0.69 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 103 HIS 0.004 0.001 HIS A 49 PHE 0.017 0.002 PHE A 268 TYR 0.018 0.002 TYR C 91 ARG 0.003 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 68 time to evaluate : 0.616 Fit side-chains REVERT: A 41 LYS cc_start: 0.7965 (mttt) cc_final: 0.7271 (mmtt) REVERT: A 153 MET cc_start: 0.7840 (mtp) cc_final: 0.7527 (mtt) outliers start: 9 outliers final: 8 residues processed: 72 average time/residue: 0.1542 time to fit residues: 14.9668 Evaluate side-chains 69 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 52 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 62 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 50 optimal weight: 0.2980 chunk 47 optimal weight: 0.4980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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: 0.8024 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 5250 Z= 0.367 Angle : 0.601 8.950 7187 Z= 0.308 Chirality : 0.047 0.209 847 Planarity : 0.004 0.031 934 Dihedral : 5.818 51.834 1004 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.36 % Allowed : 6.60 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.97 (0.32), residues: 699 helix: 1.87 (1.60), residues: 11 sheet: 1.09 (0.30), residues: 296 loop : 0.35 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 47 HIS 0.004 0.002 HIS A 49 PHE 0.019 0.003 PHE A 268 TYR 0.019 0.002 TYR C 91 ARG 0.003 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 0.548 Fit side-chains REVERT: A 41 LYS cc_start: 0.8142 (mttt) cc_final: 0.7391 (mmtt) REVERT: A 100 ILE cc_start: 0.8647 (mt) cc_final: 0.8407 (mt) REVERT: A 153 MET cc_start: 0.7913 (mtp) cc_final: 0.7665 (mtp) REVERT: A 220 PHE cc_start: 0.8269 (t80) cc_final: 0.8053 (t80) outliers start: 10 outliers final: 8 residues processed: 74 average time/residue: 0.1629 time to fit residues: 16.0055 Evaluate side-chains 79 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 66 optimal weight: 50.0000 chunk 59 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 chunk 55 optimal weight: 30.0000 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5250 Z= 0.242 Angle : 0.520 7.558 7187 Z= 0.266 Chirality : 0.045 0.193 847 Planarity : 0.004 0.032 934 Dihedral : 4.938 52.292 1004 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.36 % Allowed : 8.02 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.32), residues: 699 helix: 1.92 (1.66), residues: 11 sheet: 0.93 (0.31), residues: 297 loop : 0.23 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 47 HIS 0.003 0.001 HIS A 49 PHE 0.013 0.002 PHE A 268 TYR 0.014 0.001 TYR C 91 ARG 0.002 0.000 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 0.589 Fit side-chains REVERT: A 41 LYS cc_start: 0.8134 (mttt) cc_final: 0.7353 (mmtt) REVERT: A 153 MET cc_start: 0.7913 (mtp) cc_final: 0.7454 (mtt) REVERT: A 188 ASN cc_start: 0.7606 (OUTLIER) cc_final: 0.7282 (p0) outliers start: 10 outliers final: 7 residues processed: 73 average time/residue: 0.1357 time to fit residues: 13.6921 Evaluate side-chains 70 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 62 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 16 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 chunk 60 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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: 0.8046 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5250 Z= 0.312 Angle : 0.558 6.932 7187 Z= 0.286 Chirality : 0.046 0.207 847 Planarity : 0.004 0.032 934 Dihedral : 4.894 51.931 1004 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.07 % Allowed : 7.55 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.32), residues: 699 helix: 1.83 (1.67), residues: 11 sheet: 0.99 (0.31), residues: 291 loop : 0.03 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 47 HIS 0.003 0.001 HIS A 49 PHE 0.016 0.002 PHE A 268 TYR 0.015 0.002 TYR C 91 ARG 0.003 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 60 time to evaluate : 0.548 Fit side-chains REVERT: A 41 LYS cc_start: 0.8190 (mttt) cc_final: 0.7390 (mmtt) REVERT: A 153 MET cc_start: 0.7970 (mtp) cc_final: 0.7583 (mtp) outliers start: 13 outliers final: 10 residues processed: 68 average time/residue: 0.1659 time to fit residues: 15.0452 Evaluate side-chains 69 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 59 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 66 optimal weight: 50.0000 chunk 55 optimal weight: 30.0000 chunk 30 optimal weight: 0.0070 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 64 optimal weight: 0.0050 chunk 7 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 overall best weight: 0.5412 ------------------------------------------------------------------------------- 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: 0.8010 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5250 Z= 0.169 Angle : 0.490 6.426 7187 Z= 0.250 Chirality : 0.044 0.186 847 Planarity : 0.004 0.032 934 Dihedral : 4.574 52.697 1004 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.59 % Allowed : 7.55 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.71 (0.32), residues: 699 helix: 1.93 (1.70), residues: 11 sheet: 1.04 (0.31), residues: 294 loop : 0.05 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 47 HIS 0.002 0.001 HIS A 49 PHE 0.010 0.001 PHE B 50 TYR 0.010 0.001 TYR A 170 ARG 0.001 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 69 time to evaluate : 0.592 Fit side-chains REVERT: A 41 LYS cc_start: 0.8133 (mttt) cc_final: 0.7364 (mmtt) REVERT: A 153 MET cc_start: 0.7861 (mtp) cc_final: 0.7519 (mtp) REVERT: A 188 ASN cc_start: 0.7757 (OUTLIER) cc_final: 0.7471 (p0) outliers start: 11 outliers final: 8 residues processed: 75 average time/residue: 0.1621 time to fit residues: 16.1653 Evaluate side-chains 76 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 63 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 0.0980 chunk 37 optimal weight: 0.9980 chunk 56 optimal weight: 20.0000 chunk 66 optimal weight: 50.0000 chunk 41 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.8019 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5250 Z= 0.193 Angle : 0.497 6.073 7187 Z= 0.254 Chirality : 0.044 0.187 847 Planarity : 0.004 0.033 934 Dihedral : 4.528 52.690 1004 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.07 % Allowed : 7.78 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.76 (0.32), residues: 699 helix: 1.83 (1.67), residues: 11 sheet: 1.06 (0.31), residues: 294 loop : 0.10 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 47 HIS 0.003 0.001 HIS A 146 PHE 0.010 0.001 PHE A 92 TYR 0.011 0.001 TYR A 258 ARG 0.001 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 0.595 Fit side-chains REVERT: A 41 LYS cc_start: 0.8174 (mttt) cc_final: 0.7401 (mmtt) REVERT: A 153 MET cc_start: 0.7865 (mtp) cc_final: 0.7509 (mtp) REVERT: A 188 ASN cc_start: 0.7822 (OUTLIER) cc_final: 0.7568 (p0) outliers start: 13 outliers final: 12 residues processed: 72 average time/residue: 0.2011 time to fit residues: 19.4585 Evaluate side-chains 77 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 52 optimal weight: 20.0000 chunk 60 optimal weight: 0.4980 chunk 63 optimal weight: 0.0970 chunk 58 optimal weight: 4.9990 chunk 61 optimal weight: 0.4980 chunk 37 optimal weight: 0.6980 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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: 0.8004 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5250 Z= 0.160 Angle : 0.485 6.049 7187 Z= 0.246 Chirality : 0.044 0.178 847 Planarity : 0.004 0.032 934 Dihedral : 4.423 53.409 1004 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.59 % Allowed : 8.25 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.84 (0.33), residues: 699 helix: 1.94 (1.67), residues: 11 sheet: 1.22 (0.31), residues: 294 loop : 0.04 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 47 HIS 0.003 0.001 HIS A 146 PHE 0.008 0.001 PHE A 92 TYR 0.010 0.001 TYR A 170 ARG 0.003 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 0.601 Fit side-chains REVERT: A 41 LYS cc_start: 0.8167 (mttt) cc_final: 0.7396 (mmtt) REVERT: A 153 MET cc_start: 0.7804 (mtp) cc_final: 0.7464 (mtp) REVERT: A 188 ASN cc_start: 0.7810 (OUTLIER) cc_final: 0.7563 (p0) outliers start: 11 outliers final: 10 residues processed: 72 average time/residue: 0.1423 time to fit residues: 14.1950 Evaluate side-chains 77 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 63 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 65 optimal weight: 20.0000 chunk 39 optimal weight: 0.0270 chunk 31 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 overall best weight: 1.1644 ------------------------------------------------------------------------------- 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: 0.8059 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5250 Z= 0.333 Angle : 0.567 7.405 7187 Z= 0.288 Chirality : 0.046 0.204 847 Planarity : 0.004 0.033 934 Dihedral : 4.838 51.839 1004 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.07 % Allowed : 8.49 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.68 (0.32), residues: 699 helix: 1.76 (1.63), residues: 11 sheet: 1.17 (0.31), residues: 290 loop : -0.09 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 47 HIS 0.003 0.001 HIS A 146 PHE 0.016 0.002 PHE A 268 TYR 0.014 0.002 TYR A 258 ARG 0.005 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 67 time to evaluate : 0.960 Fit side-chains REVERT: A 41 LYS cc_start: 0.8253 (mttt) cc_final: 0.7433 (mmtt) REVERT: A 153 MET cc_start: 0.7892 (mtp) cc_final: 0.7568 (mtp) outliers start: 13 outliers final: 13 residues processed: 74 average time/residue: 0.1697 time to fit residues: 16.4745 Evaluate side-chains 75 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 62 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 54 optimal weight: 30.0000 chunk 5 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 50 optimal weight: 0.0870 chunk 8 optimal weight: 0.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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: 0.8026 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5250 Z= 0.182 Angle : 0.510 7.304 7187 Z= 0.256 Chirality : 0.044 0.194 847 Planarity : 0.004 0.033 934 Dihedral : 4.664 52.905 1004 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.83 % Allowed : 8.49 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.32), residues: 699 helix: 1.86 (1.66), residues: 11 sheet: 1.28 (0.31), residues: 290 loop : -0.03 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 47 HIS 0.003 0.001 HIS A 146 PHE 0.009 0.001 PHE B 50 TYR 0.010 0.001 TYR A 258 ARG 0.002 0.000 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 58 time to evaluate : 0.691 Fit side-chains REVERT: A 41 LYS cc_start: 0.8230 (mttt) cc_final: 0.7369 (mmtt) REVERT: A 153 MET cc_start: 0.7815 (mtp) cc_final: 0.7521 (mtp) outliers start: 12 outliers final: 12 residues processed: 66 average time/residue: 0.1664 time to fit residues: 14.6464 Evaluate side-chains 76 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 0.9990 chunk 54 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 56 optimal weight: 0.0980 chunk 6 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 48 optimal weight: 20.0000 chunk 3 optimal weight: 4.9990 chunk 39 optimal weight: 0.0470 chunk 62 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.193597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.125457 restraints weight = 5589.333| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.71 r_work: 0.3028 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5250 Z= 0.158 Angle : 0.494 7.532 7187 Z= 0.248 Chirality : 0.044 0.181 847 Planarity : 0.004 0.033 934 Dihedral : 4.521 53.544 1004 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.36 % Allowed : 9.67 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.96 (0.33), residues: 699 helix: 1.92 (1.64), residues: 11 sheet: 1.39 (0.31), residues: 291 loop : 0.07 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 47 HIS 0.002 0.001 HIS B 35 PHE 0.009 0.001 PHE A 92 TYR 0.010 0.001 TYR A 170 ARG 0.002 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1857.01 seconds wall clock time: 34 minutes 51.49 seconds (2091.49 seconds total)