Starting phenix.real_space_refine on Sat May 10 04:47:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vyf_43659/05_2025/8vyf_43659.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vyf_43659/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8vyf_43659/05_2025/8vyf_43659.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vyf_43659/05_2025/8vyf_43659.map" model { file = "/net/cci-nas-00/data/ceres_data/8vyf_43659/05_2025/8vyf_43659.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vyf_43659/05_2025/8vyf_43659.cif" } 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. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 5.37, per 1000 atoms: 1.05 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: 1.25 Conformation dependent library (CDL) restraints added in 675.7 milliseconds 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: 1.27 Time building geometry restraints manager: 1.46 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: 9.520 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: 0.020 Extract box with map and model: 0.780 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.270 Find NCS groups from input model: 0.070 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.510 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd link_NAG-ASN : bond 0.05522 ( 8) link_NAG-ASN : angle 2.14301 ( 24) link_BETA1-4 : bond 0.06307 ( 4) link_BETA1-4 : angle 2.62428 ( 12) hydrogen bonds : bond 0.17603 ( 154) hydrogen bonds : angle 8.23995 ( 369) SS BOND : bond 0.00450 ( 7) SS BOND : angle 2.77034 ( 14) covalent geometry : bond 0.01018 ( 5250) covalent geometry : angle 1.27394 ( 7187) *********************** 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 : 0.583 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: 0.1934 time to fit residues: 25.6974 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 : 0.592 ------------------------------------------------------------------------------- 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: 0.9980 chunk 52 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 54 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 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 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 = 0.4245 r_free = 0.4245 target = 0.200180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.131714 restraints weight = 5633.766| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.88 r_work: 0.3018 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5269 Z= 0.167 Angle : 0.594 7.759 7237 Z= 0.305 Chirality : 0.046 0.196 847 Planarity : 0.004 0.029 934 Dihedral : 7.560 66.864 1004 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 0.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.12 % Allowed : 5.90 % Favored : 91.98 % 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: 1.27 (0.32), residues: 699 helix: 1.57 (1.51), residues: 11 sheet: 1.17 (0.30), residues: 307 loop : 0.67 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 103 HIS 0.004 0.001 HIS A 49 PHE 0.017 0.002 PHE A 268 TYR 0.019 0.002 TYR C 91 ARG 0.004 0.001 ARG B 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00277 ( 8) link_NAG-ASN : angle 1.63474 ( 24) link_BETA1-4 : bond 0.00302 ( 4) link_BETA1-4 : angle 1.85692 ( 12) hydrogen bonds : bond 0.03414 ( 154) hydrogen bonds : angle 6.41297 ( 369) SS BOND : bond 0.00290 ( 7) SS BOND : angle 0.72741 ( 14) covalent geometry : bond 0.00406 ( 5250) covalent geometry : angle 0.58229 ( 7187) *********************** 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 78 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.522 Fit side-chains REVERT: A 41 LYS cc_start: 0.8733 (mttt) cc_final: 0.7528 (mmtt) REVERT: A 153 MET cc_start: 0.7731 (mtp) cc_final: 0.7150 (mtt) outliers start: 9 outliers final: 8 residues processed: 73 average time/residue: 0.1553 time to fit residues: 14.9964 Evaluate side-chains 69 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 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 13 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 51 optimal weight: 0.0570 chunk 47 optimal weight: 0.0870 chunk 62 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.5476 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.199696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.131443 restraints weight = 5673.760| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.61 r_work: 0.3022 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5269 Z= 0.116 Angle : 0.527 7.746 7237 Z= 0.268 Chirality : 0.045 0.179 847 Planarity : 0.004 0.032 934 Dihedral : 5.644 51.682 1004 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.42 % Allowed : 6.84 % 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: 1.24 (0.33), residues: 699 helix: 2.04 (1.62), residues: 11 sheet: 1.21 (0.31), residues: 296 loop : 0.60 (0.33), residues: 392 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 0.010 0.002 PHE A 92 TYR 0.015 0.001 TYR C 91 ARG 0.002 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 8) link_NAG-ASN : angle 1.45222 ( 24) link_BETA1-4 : bond 0.00532 ( 4) link_BETA1-4 : angle 1.67115 ( 12) hydrogen bonds : bond 0.02945 ( 154) hydrogen bonds : angle 5.77694 ( 369) SS BOND : bond 0.00186 ( 7) SS BOND : angle 0.70985 ( 14) covalent geometry : bond 0.00272 ( 5250) covalent geometry : angle 0.51676 ( 7187) *********************** 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 69 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.558 Fit side-chains REVERT: A 41 LYS cc_start: 0.8834 (mttt) cc_final: 0.7576 (mmtt) REVERT: A 153 MET cc_start: 0.7993 (mtp) cc_final: 0.7476 (mtp) REVERT: A 188 ASN cc_start: 0.8057 (OUTLIER) cc_final: 0.7309 (p0) outliers start: 6 outliers final: 5 residues processed: 67 average time/residue: 0.1487 time to fit residues: 13.4696 Evaluate side-chains 68 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 63 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 19 optimal weight: 0.0270 chunk 4 optimal weight: 0.3980 chunk 66 optimal weight: 50.0000 chunk 56 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 chunk 5 optimal weight: 0.0370 chunk 28 optimal weight: 0.5980 chunk 34 optimal weight: 0.4980 chunk 25 optimal weight: 0.4980 overall best weight: 0.2916 ------------------------------------------------------------------------------- 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 = 0.4218 r_free = 0.4218 target = 0.198338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.128660 restraints weight = 5701.612| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.87 r_work: 0.3078 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5269 Z= 0.085 Angle : 0.476 8.088 7237 Z= 0.240 Chirality : 0.043 0.164 847 Planarity : 0.004 0.033 934 Dihedral : 4.501 53.626 1004 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 0.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.94 % Allowed : 7.78 % 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 (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: 1.22 (0.33), residues: 699 helix: 2.26 (1.66), residues: 11 sheet: 1.18 (0.31), residues: 298 loop : 0.59 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 47 HIS 0.002 0.001 HIS A 49 PHE 0.008 0.001 PHE A 92 TYR 0.011 0.001 TYR A 170 ARG 0.002 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00234 ( 8) link_NAG-ASN : angle 1.35717 ( 24) link_BETA1-4 : bond 0.00442 ( 4) link_BETA1-4 : angle 1.48004 ( 12) hydrogen bonds : bond 0.02372 ( 154) hydrogen bonds : angle 5.31295 ( 369) SS BOND : bond 0.00175 ( 7) SS BOND : angle 0.43961 ( 14) covalent geometry : bond 0.00186 ( 5250) covalent geometry : angle 0.46710 ( 7187) *********************** 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 73 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.590 Fit side-chains REVERT: A 41 LYS cc_start: 0.8750 (mttt) cc_final: 0.7472 (mmtt) REVERT: A 153 MET cc_start: 0.7877 (mtp) cc_final: 0.7338 (mtp) outliers start: 4 outliers final: 4 residues processed: 71 average time/residue: 0.1419 time to fit residues: 13.7472 Evaluate side-chains 69 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 63 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 3 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 18 optimal weight: 0.2980 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.4170 r_free = 0.4170 target = 0.193347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.126816 restraints weight = 5672.833| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.95 r_work: 0.3079 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5269 Z= 0.181 Angle : 0.567 6.399 7237 Z= 0.288 Chirality : 0.046 0.197 847 Planarity : 0.004 0.033 934 Dihedral : 4.656 52.139 1004 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.07 % Allowed : 6.60 % 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 (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: 1.77 (1.59), residues: 11 sheet: 1.10 (0.31), residues: 294 loop : 0.35 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 47 HIS 0.004 0.001 HIS A 49 PHE 0.017 0.002 PHE A 268 TYR 0.015 0.002 TYR C 91 ARG 0.003 0.001 ARG B 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 8) link_NAG-ASN : angle 1.48306 ( 24) link_BETA1-4 : bond 0.00441 ( 4) link_BETA1-4 : angle 1.38502 ( 12) hydrogen bonds : bond 0.03124 ( 154) hydrogen bonds : angle 5.47804 ( 369) SS BOND : bond 0.00309 ( 7) SS BOND : angle 0.68308 ( 14) covalent geometry : bond 0.00449 ( 5250) covalent geometry : angle 0.55865 ( 7187) *********************** 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 80 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.595 Fit side-chains REVERT: A 41 LYS cc_start: 0.8853 (mttt) cc_final: 0.7529 (mmtt) REVERT: A 153 MET cc_start: 0.7989 (mtp) cc_final: 0.7492 (mtp) REVERT: A 172 SER cc_start: 0.7861 (t) cc_final: 0.7635 (t) REVERT: C 17 ASP cc_start: 0.6386 (m-30) cc_final: 0.6064 (m-30) outliers start: 13 outliers final: 10 residues processed: 74 average time/residue: 0.1614 time to fit residues: 15.9058 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 : 0.571 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 23 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 49 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 30 optimal weight: 0.4980 chunk 21 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4178 r_free = 0.4178 target = 0.194317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.125402 restraints weight = 5606.462| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.96 r_work: 0.2999 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5269 Z= 0.130 Angle : 0.512 6.164 7237 Z= 0.261 Chirality : 0.045 0.187 847 Planarity : 0.004 0.032 934 Dihedral : 4.507 52.986 1004 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.12 % Allowed : 7.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.32), residues: 699 helix: 1.80 (1.63), residues: 11 sheet: 1.15 (0.31), residues: 296 loop : 0.25 (0.32), residues: 392 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 0.011 0.002 PHE A 92 TYR 0.010 0.001 TYR C 91 ARG 0.002 0.000 ARG B 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00191 ( 8) link_NAG-ASN : angle 1.42043 ( 24) link_BETA1-4 : bond 0.00405 ( 4) link_BETA1-4 : angle 1.40498 ( 12) hydrogen bonds : bond 0.02697 ( 154) hydrogen bonds : angle 5.32766 ( 369) SS BOND : bond 0.00178 ( 7) SS BOND : angle 0.51061 ( 14) covalent geometry : bond 0.00315 ( 5250) covalent geometry : angle 0.50346 ( 7187) *********************** 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 71 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.577 Fit side-chains REVERT: A 41 LYS cc_start: 0.8822 (mttt) cc_final: 0.7527 (mmtt) REVERT: A 153 MET cc_start: 0.7916 (mtp) cc_final: 0.7416 (mtp) REVERT: A 172 SER cc_start: 0.7718 (t) cc_final: 0.7510 (t) REVERT: C 17 ASP cc_start: 0.6370 (m-30) cc_final: 0.6069 (m-30) outliers start: 9 outliers final: 8 residues processed: 66 average time/residue: 0.1827 time to fit residues: 15.6335 Evaluate side-chains 67 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 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 58 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 4 optimal weight: 0.5980 chunk 53 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4173 r_free = 0.4173 target = 0.193801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.127825 restraints weight = 5652.398| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.02 r_work: 0.3122 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3036 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= 0.134 Angle : 0.509 5.944 7237 Z= 0.259 Chirality : 0.045 0.189 847 Planarity : 0.004 0.033 934 Dihedral : 4.500 53.190 1004 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.89 % Allowed : 8.25 % 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: 0.92 (0.33), residues: 699 helix: 1.65 (1.61), residues: 11 sheet: 1.16 (0.31), residues: 292 loop : 0.24 (0.32), residues: 396 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 0.012 0.002 PHE A 268 TYR 0.010 0.001 TYR A 258 ARG 0.002 0.000 ARG B 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00187 ( 8) link_NAG-ASN : angle 1.40091 ( 24) link_BETA1-4 : bond 0.00423 ( 4) link_BETA1-4 : angle 1.36915 ( 12) hydrogen bonds : bond 0.02675 ( 154) hydrogen bonds : angle 5.23975 ( 369) SS BOND : bond 0.00203 ( 7) SS BOND : angle 0.53847 ( 14) covalent geometry : bond 0.00328 ( 5250) covalent geometry : angle 0.50054 ( 7187) *********************** 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 64 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.604 Fit side-chains REVERT: A 41 LYS cc_start: 0.8858 (mttt) cc_final: 0.7526 (mmtt) REVERT: A 153 MET cc_start: 0.7918 (mtp) cc_final: 0.7288 (mtp) REVERT: A 172 SER cc_start: 0.7808 (t) cc_final: 0.7601 (t) REVERT: C 17 ASP cc_start: 0.6354 (m-30) cc_final: 0.6051 (m-30) outliers start: 8 outliers final: 8 residues processed: 60 average time/residue: 0.1655 time to fit residues: 13.5659 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 : 0.593 ------------------------------------------------------------------------------- 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 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 36 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 65 optimal weight: 40.0000 chunk 55 optimal weight: 30.0000 chunk 63 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 66 optimal weight: 20.0000 chunk 47 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.4123 r_free = 0.4123 target = 0.188950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.119640 restraints weight = 5663.428| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.90 r_work: 0.3042 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.056 5269 Z= 0.350 Angle : 0.696 9.040 7237 Z= 0.354 Chirality : 0.051 0.251 847 Planarity : 0.005 0.033 934 Dihedral : 5.602 51.781 1004 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.36 % Allowed : 8.25 % 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: 0.42 (0.32), residues: 699 helix: 1.32 (1.64), residues: 11 sheet: 0.77 (0.30), residues: 302 loop : -0.09 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 251 HIS 0.005 0.002 HIS A 146 PHE 0.027 0.003 PHE A 268 TYR 0.021 0.003 TYR A 37 ARG 0.005 0.001 ARG B 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 8) link_NAG-ASN : angle 1.82919 ( 24) link_BETA1-4 : bond 0.00422 ( 4) link_BETA1-4 : angle 1.62386 ( 12) hydrogen bonds : bond 0.04098 ( 154) hydrogen bonds : angle 5.87282 ( 369) SS BOND : bond 0.00354 ( 7) SS BOND : angle 0.95940 ( 14) covalent geometry : bond 0.00882 ( 5250) covalent geometry : angle 0.68600 ( 7187) *********************** 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 73 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.592 Fit side-chains REVERT: A 41 LYS cc_start: 0.8905 (mttt) cc_final: 0.7492 (mmtt) REVERT: A 98 SER cc_start: 0.8328 (m) cc_final: 0.7927 (p) REVERT: A 153 MET cc_start: 0.8066 (mtp) cc_final: 0.7113 (mtt) REVERT: C 17 ASP cc_start: 0.6679 (m-30) cc_final: 0.6328 (m-30) outliers start: 10 outliers final: 10 residues processed: 68 average time/residue: 0.1714 time to fit residues: 15.2654 Evaluate side-chains 65 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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 76 LYS 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 9 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 1 optimal weight: 0.0970 chunk 56 optimal weight: 20.0000 chunk 51 optimal weight: 8.9990 chunk 13 optimal weight: 0.0870 chunk 55 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 overall best weight: 0.5756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.193147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.128144 restraints weight = 5631.759| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.89 r_work: 0.3046 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5269 Z= 0.121 Angle : 0.523 6.617 7237 Z= 0.264 Chirality : 0.045 0.216 847 Planarity : 0.004 0.033 934 Dihedral : 5.016 53.670 1004 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.36 % Allowed : 8.49 % 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: 0.64 (0.33), residues: 699 helix: 1.72 (1.67), residues: 11 sheet: 0.96 (0.31), residues: 296 loop : 0.03 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 36 HIS 0.003 0.001 HIS A 146 PHE 0.010 0.001 PHE B 50 TYR 0.010 0.001 TYR A 170 ARG 0.002 0.000 ARG B 52 Details of bonding type rmsd link_NAG-ASN : bond 0.00193 ( 8) link_NAG-ASN : angle 1.56048 ( 24) link_BETA1-4 : bond 0.00363 ( 4) link_BETA1-4 : angle 1.53594 ( 12) hydrogen bonds : bond 0.02752 ( 154) hydrogen bonds : angle 5.41682 ( 369) SS BOND : bond 0.00206 ( 7) SS BOND : angle 0.50500 ( 14) covalent geometry : bond 0.00290 ( 5250) covalent geometry : angle 0.51259 ( 7187) *********************** 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 67 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.594 Fit side-chains REVERT: A 41 LYS cc_start: 0.8854 (mttt) cc_final: 0.7471 (mmtt) REVERT: A 153 MET cc_start: 0.8013 (mtp) cc_final: 0.7333 (mtp) REVERT: C 17 ASP cc_start: 0.6477 (m-30) cc_final: 0.6164 (m-30) outliers start: 10 outliers final: 10 residues processed: 62 average time/residue: 0.1695 time to fit residues: 13.8069 Evaluate side-chains 66 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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 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 18 ARG Chi-restraints excluded: chain C residue 22 THR 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 5 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 62 optimal weight: 20.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4134 r_free = 0.4134 target = 0.190295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.122463 restraints weight = 5596.008| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.67 r_work: 0.3122 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5269 Z= 0.162 Angle : 0.538 6.717 7237 Z= 0.273 Chirality : 0.045 0.217 847 Planarity : 0.004 0.034 934 Dihedral : 5.033 53.369 1004 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.36 % Allowed : 8.49 % 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: 0.59 (0.33), residues: 699 helix: 1.62 (1.64), residues: 11 sheet: 1.06 (0.31), residues: 290 loop : -0.12 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 47 HIS 0.003 0.001 HIS A 146 PHE 0.014 0.002 PHE A 268 TYR 0.012 0.001 TYR A 170 ARG 0.003 0.000 ARG B 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00194 ( 8) link_NAG-ASN : angle 1.56310 ( 24) link_BETA1-4 : bond 0.00408 ( 4) link_BETA1-4 : angle 1.47013 ( 12) hydrogen bonds : bond 0.02909 ( 154) hydrogen bonds : angle 5.31721 ( 369) SS BOND : bond 0.00212 ( 7) SS BOND : angle 0.57063 ( 14) covalent geometry : bond 0.00399 ( 5250) covalent geometry : angle 0.52824 ( 7187) ********************** 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 69 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.579 Fit side-chains REVERT: A 41 LYS cc_start: 0.8847 (mttt) cc_final: 0.7447 (mmtt) REVERT: A 98 SER cc_start: 0.8308 (m) cc_final: 0.7919 (p) REVERT: A 153 MET cc_start: 0.7948 (mtp) cc_final: 0.7262 (mtp) REVERT: C 17 ASP cc_start: 0.6442 (m-30) cc_final: 0.6132 (m-30) outliers start: 10 outliers final: 9 residues processed: 64 average time/residue: 0.1799 time to fit residues: 15.1352 Evaluate side-chains 67 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 A residue 282 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 22 THR 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 8 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 65 optimal weight: 40.0000 chunk 56 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4139 r_free = 0.4139 target = 0.190810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.123198 restraints weight = 5649.014| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.61 r_work: 0.3002 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5269 Z= 0.147 Angle : 0.525 7.588 7237 Z= 0.265 Chirality : 0.045 0.210 847 Planarity : 0.004 0.034 934 Dihedral : 4.979 53.633 1004 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.12 % Allowed : 9.20 % 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: 0.64 (0.33), residues: 699 helix: 1.65 (1.65), residues: 11 sheet: 1.14 (0.31), residues: 290 loop : -0.12 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 47 HIS 0.003 0.001 HIS A 66 PHE 0.011 0.002 PHE A 268 TYR 0.012 0.001 TYR A 170 ARG 0.002 0.000 ARG B 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00229 ( 8) link_NAG-ASN : angle 1.49653 ( 24) link_BETA1-4 : bond 0.00390 ( 4) link_BETA1-4 : angle 1.44638 ( 12) hydrogen bonds : bond 0.02786 ( 154) hydrogen bonds : angle 5.21353 ( 369) SS BOND : bond 0.00211 ( 7) SS BOND : angle 0.50152 ( 14) covalent geometry : bond 0.00361 ( 5250) covalent geometry : angle 0.51604 ( 7187) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3389.60 seconds wall clock time: 60 minutes 14.55 seconds (3614.55 seconds total)