Starting phenix.real_space_refine on Wed Sep 17 05:24:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vyf_43659/09_2025/8vyf_43659.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vyf_43659/09_2025/8vyf_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 { model { file = "/net/cci-nas-00/data/ceres_data/8vyf_43659/09_2025/8vyf_43659.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vyf_43659/09_2025/8vyf_43659.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vyf_43659/09_2025/8vyf_43659.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vyf_43659/09_2025/8vyf_43659.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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, 'ARG:plan': 2, 'PHE: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: {'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1} 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: {'GLU:plan': 3, 'GLN:plan1': 4, 'PHE:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 3, 'ARG:plan': 2, 'TYR:plan': 4, 'ASP:plan': 7, 'HIS:plan': 1} 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: {'TYR:plan': 6, 'GLU:plan': 5, 'GLN:plan1': 8, 'ASP:plan': 5, 'TRP:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 2, 'PHE: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: 1.48, per 1000 atoms: 0.29 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 - 3.00 Amino acid : True - 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: 0.50 Conformation dependent library (CDL) restraints added in 227.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.20 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: 0.81 Time building geometry restraints manager: 0.64 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: 0.00 - 1.62: 6172 1.62 - 3.23: 825 3.23 - 4.85: 103 4.85 - 6.47: 64 6.47 - 8.08: 23 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 3.120 nonbonded pdb=" OG SER A 172 " pdb=" N GLN A 173 " model vdw 2.616 3.120 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 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 15.950 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.130 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.550 ------------------------------------------------------------------------------- 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 : 0.011 0.065 5269 Z= 0.575 Angle : 1.286 8.084 7237 Z= 0.856 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG C 61 TYR 0.026 0.004 TYR A 144 PHE 0.015 0.003 PHE A 55 TRP 0.022 0.004 TRP B 47 HIS 0.005 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.01018 ( 5250) covalent geometry : angle 1.27394 ( 7187) SS BOND : bond 0.00450 ( 7) SS BOND : angle 2.77034 ( 14) hydrogen bonds : bond 0.17603 ( 154) hydrogen bonds : angle 8.23995 ( 369) link_BETA1-4 : bond 0.06307 ( 4) link_BETA1-4 : angle 2.62428 ( 12) link_NAG-ASN : bond 0.05522 ( 8) link_NAG-ASN : angle 2.14301 ( 24) *********************** 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 to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.187 Fit side-chains REVERT: A 41 LYS cc_start: 0.7842 (mttt) cc_final: 0.7270 (mmtt) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.0822 time to fit residues: 11.0226 Evaluate side-chains 66 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.195631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.124190 restraints weight = 5722.739| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.88 r_work: 0.2939 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.058 5269 Z= 0.347 Angle : 0.731 7.618 7237 Z= 0.382 Chirality : 0.051 0.242 847 Planarity : 0.006 0.037 934 Dihedral : 7.678 64.829 1004 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.83 % Allowed : 6.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.32), residues: 699 helix: 0.94 (1.52), residues: 11 sheet: 0.99 (0.30), residues: 302 loop : 0.41 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 19 TYR 0.020 0.003 TYR C 91 PHE 0.032 0.003 PHE A 268 TRP 0.023 0.003 TRP H 103 HIS 0.006 0.002 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00884 ( 5250) covalent geometry : angle 0.72054 ( 7187) SS BOND : bond 0.00336 ( 7) SS BOND : angle 1.06425 ( 14) hydrogen bonds : bond 0.04852 ( 154) hydrogen bonds : angle 6.49176 ( 369) link_BETA1-4 : bond 0.00829 ( 4) link_BETA1-4 : angle 2.04076 ( 12) link_NAG-ASN : bond 0.00447 ( 8) link_NAG-ASN : angle 1.70842 ( 24) *********************** 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 91 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.187 Fit side-chains REVERT: A 41 LYS cc_start: 0.8917 (mttt) cc_final: 0.7602 (mmtt) REVERT: A 153 MET cc_start: 0.8001 (mtp) cc_final: 0.7347 (mtt) REVERT: A 172 SER cc_start: 0.8064 (t) cc_final: 0.7822 (t) REVERT: A 220 PHE cc_start: 0.8557 (t80) cc_final: 0.8332 (t80) REVERT: B 76 LYS cc_start: 0.8836 (mtpp) cc_final: 0.8635 (mtpp) REVERT: C 17 ASP cc_start: 0.6502 (m-30) cc_final: 0.6145 (m-30) outliers start: 12 outliers final: 10 residues processed: 85 average time/residue: 0.0699 time to fit residues: 7.9253 Evaluate side-chains 80 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 227 VAL 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 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 45 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 1 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 55 optimal weight: 20.0000 chunk 29 optimal weight: 0.5980 chunk 59 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 188 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.194792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.126176 restraints weight = 5637.645| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.60 r_work: 0.2983 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5269 Z= 0.137 Angle : 0.549 7.875 7237 Z= 0.281 Chirality : 0.045 0.198 847 Planarity : 0.004 0.041 934 Dihedral : 6.037 52.753 1004 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.59 % Allowed : 7.31 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.32), residues: 699 helix: 1.69 (1.59), residues: 11 sheet: 0.98 (0.30), residues: 296 loop : 0.34 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 237 TYR 0.014 0.001 TYR C 91 PHE 0.012 0.002 PHE A 157 TRP 0.008 0.001 TRP B 47 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 5250) covalent geometry : angle 0.53800 ( 7187) SS BOND : bond 0.00173 ( 7) SS BOND : angle 0.68821 ( 14) hydrogen bonds : bond 0.03212 ( 154) hydrogen bonds : angle 5.89392 ( 369) link_BETA1-4 : bond 0.00482 ( 4) link_BETA1-4 : angle 1.79228 ( 12) link_NAG-ASN : bond 0.00246 ( 8) link_NAG-ASN : angle 1.52707 ( 24) *********************** 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 76 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.153 Fit side-chains REVERT: A 41 LYS cc_start: 0.8857 (mttt) cc_final: 0.7534 (mmtt) REVERT: A 153 MET cc_start: 0.7996 (mtp) cc_final: 0.7586 (mtp) REVERT: A 188 ASN cc_start: 0.8079 (OUTLIER) cc_final: 0.7720 (p0) REVERT: C 17 ASP cc_start: 0.6440 (m-30) cc_final: 0.6080 (m-30) outliers start: 11 outliers final: 9 residues processed: 71 average time/residue: 0.0724 time to fit residues: 6.8663 Evaluate side-chains 74 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.113 ------------------------------------------------------------------------------- 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 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 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 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 188 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.193280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.127404 restraints weight = 5605.440| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.95 r_work: 0.2927 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5269 Z= 0.162 Angle : 0.543 7.548 7237 Z= 0.276 Chirality : 0.045 0.203 847 Planarity : 0.004 0.041 934 Dihedral : 5.238 52.699 1004 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.83 % Allowed : 7.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.32), residues: 699 helix: 1.90 (1.63), residues: 11 sheet: 0.87 (0.31), residues: 295 loop : 0.23 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 190 TYR 0.013 0.001 TYR C 91 PHE 0.013 0.002 PHE B 50 TRP 0.009 0.001 TRP B 47 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 5250) covalent geometry : angle 0.53203 ( 7187) SS BOND : bond 0.00147 ( 7) SS BOND : angle 0.67523 ( 14) hydrogen bonds : bond 0.03079 ( 154) hydrogen bonds : angle 5.65492 ( 369) link_BETA1-4 : bond 0.00493 ( 4) link_BETA1-4 : angle 1.68426 ( 12) link_NAG-ASN : bond 0.00234 ( 8) link_NAG-ASN : angle 1.52427 ( 24) *********************** 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 77 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.437 Fit side-chains REVERT: A 41 LYS cc_start: 0.8845 (mttt) cc_final: 0.7467 (mmtt) REVERT: A 153 MET cc_start: 0.7857 (mtp) cc_final: 0.7086 (mtt) REVERT: A 172 SER cc_start: 0.7782 (t) cc_final: 0.7551 (t) REVERT: C 17 ASP cc_start: 0.6351 (m-30) cc_final: 0.5976 (m-30) outliers start: 12 outliers final: 9 residues processed: 72 average time/residue: 0.0792 time to fit residues: 7.3807 Evaluate side-chains 66 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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 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 3 optimal weight: 3.9990 chunk 30 optimal weight: 0.1980 chunk 12 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 24 optimal weight: 0.6980 chunk 41 optimal weight: 0.0470 chunk 1 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 overall best weight: 0.4278 ------------------------------------------------------------------------------- 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 = 0.4181 r_free = 0.4181 target = 0.194539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.129438 restraints weight = 5762.493| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.89 r_work: 0.3085 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5269 Z= 0.099 Angle : 0.497 7.122 7237 Z= 0.252 Chirality : 0.044 0.183 847 Planarity : 0.004 0.033 934 Dihedral : 4.705 53.572 1004 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.36 % Allowed : 6.37 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.32), residues: 699 helix: 2.06 (1.65), residues: 11 sheet: 0.97 (0.31), residues: 296 loop : 0.24 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 237 TYR 0.010 0.001 TYR A 170 PHE 0.011 0.001 PHE A 157 TRP 0.006 0.001 TRP B 47 HIS 0.002 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 5250) covalent geometry : angle 0.48767 ( 7187) SS BOND : bond 0.00219 ( 7) SS BOND : angle 0.51664 ( 14) hydrogen bonds : bond 0.02559 ( 154) hydrogen bonds : angle 5.38306 ( 369) link_BETA1-4 : bond 0.00417 ( 4) link_BETA1-4 : angle 1.51527 ( 12) link_NAG-ASN : bond 0.00227 ( 8) link_NAG-ASN : angle 1.44579 ( 24) *********************** 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 72 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.170 Fit side-chains REVERT: A 41 LYS cc_start: 0.8819 (mttt) cc_final: 0.7480 (mmtt) REVERT: A 153 MET cc_start: 0.7865 (mtp) cc_final: 0.7172 (mtt) REVERT: A 172 SER cc_start: 0.7722 (t) cc_final: 0.7514 (t) REVERT: C 4 MET cc_start: 0.8738 (mmm) cc_final: 0.8479 (mmm) REVERT: C 17 ASP cc_start: 0.6323 (m-30) cc_final: 0.5951 (m-30) outliers start: 10 outliers final: 9 residues processed: 70 average time/residue: 0.0788 time to fit residues: 7.2525 Evaluate side-chains 66 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.189 ------------------------------------------------------------------------------- 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 C residue 5 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 46 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 54 optimal weight: 20.0000 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.4153 r_free = 0.4153 target = 0.192055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.124120 restraints weight = 5657.552| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.58 r_work: 0.2993 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5269 Z= 0.126 Angle : 0.511 6.575 7237 Z= 0.261 Chirality : 0.044 0.188 847 Planarity : 0.004 0.031 934 Dihedral : 4.565 53.134 1004 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.12 % Allowed : 7.55 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.32), residues: 699 helix: 2.06 (1.62), residues: 11 sheet: 1.06 (0.31), residues: 291 loop : 0.13 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 237 TYR 0.011 0.001 TYR A 170 PHE 0.012 0.002 PHE A 92 TRP 0.007 0.001 TRP B 47 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 5250) covalent geometry : angle 0.50247 ( 7187) SS BOND : bond 0.00174 ( 7) SS BOND : angle 0.55070 ( 14) hydrogen bonds : bond 0.02689 ( 154) hydrogen bonds : angle 5.27796 ( 369) link_BETA1-4 : bond 0.00460 ( 4) link_BETA1-4 : angle 1.41501 ( 12) link_NAG-ASN : bond 0.00206 ( 8) link_NAG-ASN : angle 1.42730 ( 24) *********************** 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 66 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.218 Fit side-chains REVERT: A 41 LYS cc_start: 0.8794 (mttt) cc_final: 0.7424 (mmtt) REVERT: A 153 MET cc_start: 0.7866 (mtp) cc_final: 0.7157 (mtt) REVERT: A 172 SER cc_start: 0.7781 (t) cc_final: 0.7564 (t) REVERT: C 17 ASP cc_start: 0.6374 (m-30) cc_final: 0.6062 (m-30) outliers start: 9 outliers final: 8 residues processed: 63 average time/residue: 0.0746 time to fit residues: 6.2819 Evaluate side-chains 65 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 5 THR Chi-restraints excluded: chain C residue 18 ARG 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 57 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 34 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 54 optimal weight: 20.0000 chunk 43 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.191715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.122203 restraints weight = 5657.782| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.60 r_work: 0.2988 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5269 Z= 0.195 Angle : 0.566 7.402 7237 Z= 0.287 Chirality : 0.046 0.211 847 Planarity : 0.004 0.031 934 Dihedral : 4.896 52.448 1004 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.83 % Allowed : 7.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.32), residues: 699 helix: 1.82 (1.62), residues: 11 sheet: 0.89 (0.31), residues: 296 loop : 0.01 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 19 TYR 0.013 0.002 TYR A 37 PHE 0.015 0.002 PHE A 268 TRP 0.011 0.002 TRP B 47 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 5250) covalent geometry : angle 0.55619 ( 7187) SS BOND : bond 0.00237 ( 7) SS BOND : angle 0.69077 ( 14) hydrogen bonds : bond 0.03114 ( 154) hydrogen bonds : angle 5.42725 ( 369) link_BETA1-4 : bond 0.00431 ( 4) link_BETA1-4 : angle 1.46585 ( 12) link_NAG-ASN : bond 0.00253 ( 8) link_NAG-ASN : angle 1.57974 ( 24) *********************** 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 74 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.182 Fit side-chains REVERT: A 41 LYS cc_start: 0.8847 (mttt) cc_final: 0.7443 (mmtt) REVERT: A 153 MET cc_start: 0.7982 (mtp) cc_final: 0.7321 (mtp) REVERT: A 172 SER cc_start: 0.7941 (t) cc_final: 0.7741 (t) REVERT: C 17 ASP cc_start: 0.6497 (m-30) cc_final: 0.6162 (m-30) outliers start: 12 outliers final: 12 residues processed: 68 average time/residue: 0.0720 time to fit residues: 6.4617 Evaluate side-chains 71 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.186 ------------------------------------------------------------------------------- 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 A residue 282 VAL 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 C residue 5 THR Chi-restraints excluded: chain C residue 18 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 chunk 43 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 55 optimal weight: 30.0000 chunk 3 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 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 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.191547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.123265 restraints weight = 5670.093| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.64 r_work: 0.3029 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5269 Z= 0.131 Angle : 0.515 6.326 7237 Z= 0.262 Chirality : 0.045 0.200 847 Planarity : 0.004 0.033 934 Dihedral : 4.731 53.533 1004 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.59 % Allowed : 8.49 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.33), residues: 699 helix: 1.82 (1.65), residues: 11 sheet: 0.94 (0.31), residues: 296 loop : 0.10 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 19 TYR 0.011 0.001 TYR A 170 PHE 0.010 0.002 PHE A 92 TRP 0.008 0.001 TRP B 47 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 5250) covalent geometry : angle 0.50619 ( 7187) SS BOND : bond 0.00193 ( 7) SS BOND : angle 0.49516 ( 14) hydrogen bonds : bond 0.02685 ( 154) hydrogen bonds : angle 5.27083 ( 369) link_BETA1-4 : bond 0.00394 ( 4) link_BETA1-4 : angle 1.44292 ( 12) link_NAG-ASN : bond 0.00187 ( 8) link_NAG-ASN : angle 1.47102 ( 24) *********************** 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 71 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.184 Fit side-chains REVERT: A 41 LYS cc_start: 0.8816 (mttt) cc_final: 0.7427 (mmtt) REVERT: A 153 MET cc_start: 0.7950 (mtp) cc_final: 0.7340 (mtp) REVERT: C 17 ASP cc_start: 0.6462 (m-30) cc_final: 0.6145 (m-30) outliers start: 11 outliers final: 10 residues processed: 66 average time/residue: 0.0794 time to fit residues: 6.8232 Evaluate side-chains 70 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.189 ------------------------------------------------------------------------------- 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 76 LYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 18 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 56 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.190154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.121708 restraints weight = 5628.384| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.78 r_work: 0.2935 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 5269 Z= 0.258 Angle : 0.614 8.374 7237 Z= 0.311 Chirality : 0.048 0.233 847 Planarity : 0.005 0.034 934 Dihedral : 5.270 52.206 1004 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.83 % Allowed : 8.25 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.32), residues: 699 helix: 1.56 (1.64), residues: 11 sheet: 0.86 (0.30), residues: 296 loop : -0.14 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 19 TYR 0.017 0.002 TYR A 37 PHE 0.020 0.003 PHE A 268 TRP 0.013 0.002 TRP B 47 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00650 ( 5250) covalent geometry : angle 0.60410 ( 7187) SS BOND : bond 0.00249 ( 7) SS BOND : angle 0.81521 ( 14) hydrogen bonds : bond 0.03484 ( 154) hydrogen bonds : angle 5.50630 ( 369) link_BETA1-4 : bond 0.00441 ( 4) link_BETA1-4 : angle 1.51061 ( 12) link_NAG-ASN : bond 0.00294 ( 8) link_NAG-ASN : angle 1.66951 ( 24) *********************** 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 73 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.242 Fit side-chains REVERT: A 41 LYS cc_start: 0.8873 (mttt) cc_final: 0.7460 (mmtt) REVERT: A 153 MET cc_start: 0.8068 (mtp) cc_final: 0.7638 (mtp) REVERT: C 17 ASP cc_start: 0.6627 (m-30) cc_final: 0.6254 (m-30) outliers start: 12 outliers final: 12 residues processed: 68 average time/residue: 0.0807 time to fit residues: 7.1277 Evaluate side-chains 69 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.185 ------------------------------------------------------------------------------- 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 C residue 5 THR Chi-restraints excluded: chain C residue 18 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 17 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 66 optimal weight: 50.0000 chunk 20 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.189899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.124945 restraints weight = 5650.806| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.91 r_work: 0.2936 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5269 Z= 0.161 Angle : 0.546 7.220 7237 Z= 0.277 Chirality : 0.046 0.219 847 Planarity : 0.004 0.032 934 Dihedral : 5.106 53.324 1004 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.32), residues: 699 helix: 1.75 (1.67), residues: 11 sheet: 0.91 (0.31), residues: 290 loop : -0.13 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 103 TYR 0.012 0.001 TYR A 170 PHE 0.012 0.002 PHE A 220 TRP 0.009 0.001 TRP B 47 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 5250) covalent geometry : angle 0.53580 ( 7187) SS BOND : bond 0.00219 ( 7) SS BOND : angle 0.61347 ( 14) hydrogen bonds : bond 0.02967 ( 154) hydrogen bonds : angle 5.35020 ( 369) link_BETA1-4 : bond 0.00388 ( 4) link_BETA1-4 : angle 1.50123 ( 12) link_NAG-ASN : bond 0.00218 ( 8) link_NAG-ASN : angle 1.57823 ( 24) ********************** 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 72 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.195 Fit side-chains REVERT: A 41 LYS cc_start: 0.8876 (mttt) cc_final: 0.7474 (mmtt) REVERT: A 153 MET cc_start: 0.8026 (mtp) cc_final: 0.7487 (mtp) REVERT: C 17 ASP cc_start: 0.6578 (m-30) cc_final: 0.6202 (m-30) outliers start: 13 outliers final: 12 residues processed: 66 average time/residue: 0.0808 time to fit residues: 6.9408 Evaluate side-chains 71 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.179 ------------------------------------------------------------------------------- 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 A residue 282 VAL 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 C residue 5 THR Chi-restraints excluded: chain C residue 18 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 60 optimal weight: 0.0040 chunk 3 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 9 optimal weight: 0.2980 chunk 41 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.190958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.124148 restraints weight = 5711.125| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.81 r_work: 0.2988 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5269 Z= 0.120 Angle : 0.510 7.563 7237 Z= 0.257 Chirality : 0.045 0.204 847 Planarity : 0.004 0.033 934 Dihedral : 4.912 53.865 1004 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.33), residues: 699 helix: 1.67 (1.64), residues: 11 sheet: 0.99 (0.31), residues: 290 loop : -0.07 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 103 TYR 0.012 0.001 TYR A 170 PHE 0.010 0.001 PHE A 92 TRP 0.007 0.001 TRP B 47 HIS 0.002 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 5250) covalent geometry : angle 0.50076 ( 7187) SS BOND : bond 0.00167 ( 7) SS BOND : angle 0.46983 ( 14) hydrogen bonds : bond 0.02621 ( 154) hydrogen bonds : angle 5.18112 ( 369) link_BETA1-4 : bond 0.00399 ( 4) link_BETA1-4 : angle 1.43311 ( 12) link_NAG-ASN : bond 0.00206 ( 8) link_NAG-ASN : angle 1.49414 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1848.34 seconds wall clock time: 32 minutes 14.06 seconds (1934.06 seconds total)