Starting phenix.real_space_refine on Fri Jul 25 05:15:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dl7_27498/07_2025/8dl7_27498_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dl7_27498/07_2025/8dl7_27498.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dl7_27498/07_2025/8dl7_27498.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dl7_27498/07_2025/8dl7_27498.map" model { file = "/net/cci-nas-00/data/ceres_data/8dl7_27498/07_2025/8dl7_27498_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dl7_27498/07_2025/8dl7_27498_neut.cif" } resolution = 2.7 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= 0.012 sd= 0.075 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 37 5.16 5 C 4236 2.51 5 N 1094 2.21 5 O 1217 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6586 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3547 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 467, 3536 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 454} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 20 Conformer: "B" Number of residues, atoms: 467, 3536 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 454} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 3596 Chain: "C" Number of atoms: 1373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1373 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 203} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 290 Unresolved non-hydrogen angles: 372 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 154 Chain: "D" Number of atoms: 1438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1438 Classifications: {'peptide': 219} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 80} Link IDs: {'PTRANS': 14, 'TRANS': 204} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 251 Unresolved non-hydrogen angles: 335 Unresolved non-hydrogen dihedrals: 207 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 91 Chain: "F" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'SQ6:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 70 Unusual residues: {'EOE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 2} Not linked: pdbres="2GX F 4 " pdbres="EOE F 5 " Not linked: pdbres="EOE F 5 " pdbres="ARG F 6 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'2GX:plan-3': 1, 'EOE:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Unusual residues: {'3FB': 1, 'ACA': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ACA:plan-1': 1, '3FB:plan-2': 1, 'SOW:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'SQI': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE A 292 " occ=0.37 ... (20 atoms not shown) pdb=" CZ BPHE A 292 " occ=0.63 Time building chain proxies: 7.12, per 1000 atoms: 1.08 Number of scatterers: 6586 At special positions: 0 Unit cell: (83.6, 74.8, 145.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 37 16.00 P 2 15.00 O 1217 8.00 N 1094 7.00 C 4236 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS F 7 " distance=2.06 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 553 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 108 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 115 " distance=2.03 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 additional links: simple=1, symmetry=0 Simple link: pdb=" C ARG F 8 " - pdb=" N 3FB F 9 " Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 1.3 seconds 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue is complicated and confusing pdb=" CB 3FB F 9 " Number of C-beta restraints generated: 1660 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 10 sheets defined 47.3% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 13 through 21 removed outlier: 3.632A pdb=" N LEU A 17 " --> pdb=" O CYS A 13 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA A 18 " --> pdb=" O CYS A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 54 removed outlier: 3.762A pdb=" N TYR A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 84 removed outlier: 4.386A pdb=" N THR A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 removed outlier: 3.758A pdb=" N VAL A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 123 Processing helix chain 'A' and resid 126 through 164 removed outlier: 4.420A pdb=" N THR A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER A 131 " --> pdb=" O TRP A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 198 Proline residue: A 189 - end of helix Processing helix chain 'A' and resid 200 through 230 Processing helix chain 'A' and resid 231 through 234 removed outlier: 3.665A pdb=" N ALA A 234 " --> pdb=" O PRO A 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 231 through 234' Processing helix chain 'A' and resid 285 through 304 Proline residue: A 291 - end of helix Processing helix chain 'A' and resid 307 through 317 removed outlier: 3.545A pdb=" N GLY A 311 " --> pdb=" O VAL A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 336 Processing helix chain 'A' and resid 339 through 367 Processing helix chain 'A' and resid 369 through 390 removed outlier: 3.833A pdb=" N SER A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 483 removed outlier: 3.511A pdb=" N SER A 456 " --> pdb=" O ILE A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 488 through 514 removed outlier: 3.559A pdb=" N HIS A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 547 removed outlier: 3.686A pdb=" N LEU A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY A 547 " --> pdb=" O GLN A 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 103 removed outlier: 3.763A pdb=" N LEU C 103 " --> pdb=" O SER C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 147 Processing helix chain 'C' and resid 202 through 208 Processing helix chain 'D' and resid 47 through 51 Processing helix chain 'D' and resid 81 through 84 removed outlier: 3.533A pdb=" N GLN D 84 " --> pdb=" O PRO D 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 81 through 84' Processing helix chain 'D' and resid 106 through 110 removed outlier: 3.764A pdb=" N THR D 110 " --> pdb=" O SER D 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 24 through 25 removed outlier: 3.638A pdb=" N ASP C 90 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 30 through 32 removed outlier: 6.312A pdb=" N MET C 31 " --> pdb=" O GLU C 125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 73 through 74 removed outlier: 6.566A pdb=" N TRP C 55 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N TYR C 69 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL C 53 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR C 117 " --> pdb=" O GLN C 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 137 through 138 removed outlier: 3.730A pdb=" N VAL C 153 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN C 158 " --> pdb=" O TYR C 193 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N TYR C 193 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 165 through 170 removed outlier: 6.320A pdb=" N HIS C 218 " --> pdb=" O SER C 223 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N SER C 223 " --> pdb=" O HIS C 218 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 22 through 25 Processing sheet with id=AA7, first strand: chain 'D' and resid 29 through 31 removed outlier: 6.512A pdb=" N MET D 53 " --> pdb=" O TRP D 69 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TRP D 69 " --> pdb=" O MET D 53 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TRP D 55 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 145 through 146 removed outlier: 5.556A pdb=" N TYR D 200 " --> pdb=" O GLY D 169 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 145 through 146 removed outlier: 5.556A pdb=" N TYR D 200 " --> pdb=" O GLY D 169 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 176 through 179 removed outlier: 4.680A pdb=" N ILE D 218 " --> pdb=" O ILE D 235 " (cutoff:3.500A) 437 hydrogen bonds defined for protein. 1239 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 2.77 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: 1172 1.33 - 1.45: 1704 1.45 - 1.57: 3763 1.57 - 1.70: 4 1.70 - 1.82: 58 Bond restraints: 6701 Sorted by residual: bond pdb=" N SOW F 11 " pdb=" CB SOW F 11 " ideal model delta sigma weight residual 1.435 1.502 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" N VAL A 484 " pdb=" CA VAL A 484 " ideal model delta sigma weight residual 1.459 1.497 -0.039 1.19e-02 7.06e+03 1.05e+01 bond pdb=" N ILE A 485 " pdb=" CA ILE A 485 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.19e-02 7.06e+03 9.22e+00 bond pdb=" N GLU A 488 " pdb=" CA GLU A 488 " ideal model delta sigma weight residual 1.459 1.486 -0.027 9.10e-03 1.21e+04 8.85e+00 bond pdb=" N VAL A 113 " pdb=" CA VAL A 113 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.19e-02 7.06e+03 8.77e+00 ... (remaining 6696 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.96: 9092 6.96 - 13.92: 5 13.92 - 20.88: 0 20.88 - 27.85: 0 27.85 - 34.81: 1 Bond angle restraints: 9098 Sorted by residual: angle pdb=" N SOW F 11 " pdb=" CA SOW F 11 " pdb=" C SOW F 11 " ideal model delta sigma weight residual 112.87 147.68 -34.81 3.00e+00 1.11e-01 1.35e+02 angle pdb=" CA SOW F 11 " pdb=" N SOW F 11 " pdb=" CB SOW F 11 " ideal model delta sigma weight residual 114.32 100.44 13.88 3.00e+00 1.11e-01 2.14e+01 angle pdb=" C CYS F 7 " pdb=" CA CYS F 7 " pdb=" CB CYS F 7 " ideal model delta sigma weight residual 110.42 101.58 8.84 1.99e+00 2.53e-01 1.97e+01 angle pdb=" C ILE A 491 " pdb=" N ILE A 492 " pdb=" CA ILE A 492 " ideal model delta sigma weight residual 120.56 115.55 5.01 1.26e+00 6.30e-01 1.58e+01 angle pdb=" N ALA D 111 " pdb=" CA ALA D 111 " pdb=" C ALA D 111 " ideal model delta sigma weight residual 107.73 112.51 -4.78 1.34e+00 5.57e-01 1.27e+01 ... (remaining 9093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 3500 17.94 - 35.88: 296 35.88 - 53.81: 110 53.81 - 71.75: 21 71.75 - 89.69: 7 Dihedral angle restraints: 3934 sinusoidal: 1340 harmonic: 2594 Sorted by residual: dihedral pdb=" C SOW F 11 " pdb=" N SOW F 11 " pdb=" CA SOW F 11 " pdb=" CB SOW F 11 " ideal model delta harmonic sigma weight residual -122.60 -149.11 26.51 0 2.50e+00 1.60e-01 1.12e+02 dihedral pdb=" N SOW F 11 " pdb=" C SOW F 11 " pdb=" CA SOW F 11 " pdb=" CB SOW F 11 " ideal model delta harmonic sigma weight residual 122.80 100.36 22.44 0 2.50e+00 1.60e-01 8.05e+01 dihedral pdb=" C CYS F 7 " pdb=" N CYS F 7 " pdb=" CA CYS F 7 " pdb=" CB CYS F 7 " ideal model delta harmonic sigma weight residual -122.60 -109.34 -13.26 0 2.50e+00 1.60e-01 2.81e+01 ... (remaining 3931 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 940 0.076 - 0.152: 114 0.152 - 0.228: 8 0.228 - 0.305: 0 0.305 - 0.381: 1 Chirality restraints: 1063 Sorted by residual: chirality pdb=" CA CYS F 7 " pdb=" N CYS F 7 " pdb=" C CYS F 7 " pdb=" CB CYS F 7 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CB ILE A 152 " pdb=" CA ILE A 152 " pdb=" CG1 ILE A 152 " pdb=" CG2 ILE A 152 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA ILE A 485 " pdb=" N ILE A 485 " pdb=" C ILE A 485 " pdb=" CB ILE A 485 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.05e-01 ... (remaining 1060 not shown) Planarity restraints: 1145 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 155 " -0.010 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" C GLN A 155 " 0.033 2.00e-02 2.50e+03 pdb=" O GLN A 155 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG A 156 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 59 " -0.160 9.50e-02 1.11e+02 7.16e-02 3.15e+00 pdb=" NE ARG D 59 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG D 59 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG D 59 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 59 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP D 80 " 0.025 5.00e-02 4.00e+02 3.85e-02 2.38e+00 pdb=" N PRO D 81 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO D 81 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 81 " 0.021 5.00e-02 4.00e+02 ... (remaining 1142 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1200 2.77 - 3.30: 6177 3.30 - 3.84: 10308 3.84 - 4.37: 10967 4.37 - 4.90: 19837 Nonbonded interactions: 48489 Sorted by model distance: nonbonded pdb=" OD2 ASP A 504 " pdb=" CAH 2GX F 4 " model vdw 2.238 3.340 nonbonded pdb=" OG SER C 70 " pdb=" OD1 ASN C 73 " model vdw 2.281 3.040 nonbonded pdb=" OE1 GLU A 165 " pdb=" OH TYR D 51 " model vdw 2.282 3.040 nonbonded pdb=" O SER D 26 " pdb=" OG1 THR D 133 " model vdw 2.299 3.040 nonbonded pdb=" OE1 GLU C 125 " pdb=" N ILE C 126 " model vdw 2.315 3.120 ... (remaining 48484 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.37 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: 1.060 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 24.600 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:18.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 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 : 0.006 0.102 6712 Z= 0.415 Angle : 0.818 34.807 9109 Z= 0.465 Chirality : 0.050 0.381 1063 Planarity : 0.004 0.072 1144 Dihedral : 16.202 89.691 2259 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.49 % Favored : 95.28 % Rotamer: Outliers : 2.90 % Allowed : 27.13 % Favored : 69.97 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 2.86 % 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: 1.47 (0.29), residues: 893 helix: 2.03 (0.27), residues: 401 sheet: 1.39 (0.38), residues: 214 loop : -0.97 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 299 HIS 0.005 0.001 HIS A 535 PHE 0.010 0.001 PHE A 308 TYR 0.008 0.001 TYR C 160 ARG 0.003 0.000 ARG D 32 Details of bonding type rmsd link_TRANS : bond 0.00010 ( 1) link_TRANS : angle 0.43694 ( 3) hydrogen bonds : bond 0.11962 ( 428) hydrogen bonds : angle 5.76789 ( 1239) SS BOND : bond 0.01573 ( 4) SS BOND : angle 5.21673 ( 8) covalent geometry : bond 0.00497 ( 6701) covalent geometry : angle 0.80392 ( 9098) Misc. bond : bond 0.09215 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.763 Fit side-chains REVERT: A 112 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7711 (tmm) REVERT: A 194 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8258 (tm-30) REVERT: A 198 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7862 (t80) REVERT: C 125 GLU cc_start: 0.6373 (tp30) cc_final: 0.6036 (tp30) REVERT: D 108 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8466 (tm-30) outliers start: 17 outliers final: 11 residues processed: 62 average time/residue: 1.3340 time to fit residues: 87.1128 Evaluate side-chains 59 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain D residue 136 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 10.0000 chunk 66 optimal weight: 50.0000 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.073594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.049717 restraints weight = 50412.758| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 4.95 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.0842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6712 Z= 0.177 Angle : 0.728 41.630 9109 Z= 0.334 Chirality : 0.041 0.179 1063 Planarity : 0.003 0.044 1144 Dihedral : 9.123 81.452 1104 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.71 % Favored : 96.18 % Rotamer: Outliers : 4.10 % Allowed : 24.06 % Favored : 71.84 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.29), residues: 893 helix: 2.90 (0.26), residues: 402 sheet: 1.57 (0.38), residues: 214 loop : -0.88 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 69 HIS 0.006 0.001 HIS A 535 PHE 0.010 0.001 PHE A 508 TYR 0.010 0.001 TYR C 69 ARG 0.007 0.001 ARG F 8 Details of bonding type rmsd link_TRANS : bond 0.00003 ( 1) link_TRANS : angle 0.72578 ( 3) hydrogen bonds : bond 0.07151 ( 428) hydrogen bonds : angle 4.36507 ( 1239) SS BOND : bond 0.00322 ( 4) SS BOND : angle 0.85858 ( 8) covalent geometry : bond 0.00395 ( 6701) covalent geometry : angle 0.72782 ( 9098) Misc. bond : bond 0.00033 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 44 time to evaluate : 0.728 Fit side-chains REVERT: A 112 MET cc_start: 0.8013 (ttm) cc_final: 0.7775 (tmm) REVERT: D 22 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8639 (tt0) REVERT: D 108 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8463 (tm-30) REVERT: D 118 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8381 (tptp) outliers start: 24 outliers final: 9 residues processed: 64 average time/residue: 1.2194 time to fit residues: 82.5954 Evaluate side-chains 53 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 118 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 27 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 64 optimal weight: 30.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 = 0.3523 r_free = 0.3523 target = 0.073185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.049153 restraints weight = 50514.818| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 4.94 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6712 Z= 0.192 Angle : 0.740 41.864 9109 Z= 0.340 Chirality : 0.042 0.179 1063 Planarity : 0.003 0.048 1144 Dihedral : 8.587 82.927 1088 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.82 % Favored : 96.07 % Rotamer: Outliers : 4.27 % Allowed : 23.89 % Favored : 71.84 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.29), residues: 893 helix: 3.02 (0.26), residues: 403 sheet: 1.50 (0.38), residues: 214 loop : -0.92 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 69 HIS 0.005 0.001 HIS A 535 PHE 0.011 0.001 PHE A 308 TYR 0.009 0.001 TYR C 69 ARG 0.005 0.001 ARG F 8 Details of bonding type rmsd link_TRANS : bond 0.00038 ( 1) link_TRANS : angle 0.57871 ( 3) hydrogen bonds : bond 0.07396 ( 428) hydrogen bonds : angle 4.31225 ( 1239) SS BOND : bond 0.00346 ( 4) SS BOND : angle 0.83148 ( 8) covalent geometry : bond 0.00435 ( 6701) covalent geometry : angle 0.74043 ( 9098) Misc. bond : bond 0.00020 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 44 time to evaluate : 0.593 Fit side-chains REVERT: A 112 MET cc_start: 0.7900 (ttm) cc_final: 0.7643 (tmm) REVERT: A 198 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.8036 (t80) REVERT: D 22 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8642 (tt0) REVERT: D 108 GLU cc_start: 0.8839 (tm-30) cc_final: 0.8504 (tm-30) REVERT: D 118 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8456 (tptp) outliers start: 25 outliers final: 9 residues processed: 65 average time/residue: 1.2575 time to fit residues: 86.1917 Evaluate side-chains 55 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 63 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 60 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 chunk 36 optimal weight: 0.0170 chunk 77 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 87 optimal weight: 40.0000 overall best weight: 2.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 26 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.073964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.050197 restraints weight = 54145.731| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 5.11 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6712 Z= 0.151 Angle : 0.710 41.858 9109 Z= 0.324 Chirality : 0.041 0.199 1063 Planarity : 0.003 0.049 1144 Dihedral : 8.402 84.245 1088 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.82 % Favored : 96.07 % Rotamer: Outliers : 3.75 % Allowed : 25.09 % Favored : 71.16 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.29), residues: 893 helix: 3.19 (0.26), residues: 403 sheet: 1.45 (0.38), residues: 208 loop : -0.94 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 69 HIS 0.005 0.001 HIS A 535 PHE 0.009 0.001 PHE A 295 TYR 0.008 0.001 TYR C 69 ARG 0.004 0.000 ARG F 8 Details of bonding type rmsd link_TRANS : bond 0.00020 ( 1) link_TRANS : angle 0.49382 ( 3) hydrogen bonds : bond 0.06615 ( 428) hydrogen bonds : angle 4.10524 ( 1239) SS BOND : bond 0.00240 ( 4) SS BOND : angle 0.70027 ( 8) covalent geometry : bond 0.00326 ( 6701) covalent geometry : angle 0.71023 ( 9098) Misc. bond : bond 0.00023 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 46 time to evaluate : 0.753 Fit side-chains REVERT: A 112 MET cc_start: 0.7878 (ttm) cc_final: 0.7550 (tmm) REVERT: A 312 MET cc_start: 0.9312 (mmm) cc_final: 0.9103 (mmm) REVERT: D 22 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8638 (tt0) REVERT: D 108 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8512 (tm-30) REVERT: D 118 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8419 (tptp) REVERT: F 6 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.6998 (mmm160) outliers start: 22 outliers final: 10 residues processed: 63 average time/residue: 1.3506 time to fit residues: 89.7745 Evaluate side-chains 56 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain F residue 6 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 23 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 57 optimal weight: 40.0000 chunk 61 optimal weight: 50.0000 chunk 14 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 58 optimal weight: 30.0000 chunk 2 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.7182 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.074475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.050917 restraints weight = 49661.698| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 4.93 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6712 Z= 0.140 Angle : 0.732 41.843 9109 Z= 0.327 Chirality : 0.041 0.194 1063 Planarity : 0.003 0.049 1144 Dihedral : 8.332 84.959 1088 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.71 % Favored : 96.18 % Rotamer: Outliers : 3.41 % Allowed : 25.26 % Favored : 71.33 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.29), residues: 893 helix: 3.19 (0.26), residues: 402 sheet: 1.45 (0.38), residues: 208 loop : -0.90 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 69 HIS 0.004 0.001 HIS A 535 PHE 0.010 0.001 PHE A 295 TYR 0.008 0.001 TYR C 69 ARG 0.003 0.000 ARG F 8 Details of bonding type rmsd link_TRANS : bond 0.00022 ( 1) link_TRANS : angle 0.45090 ( 3) hydrogen bonds : bond 0.06273 ( 428) hydrogen bonds : angle 4.02174 ( 1239) SS BOND : bond 0.00300 ( 4) SS BOND : angle 0.68979 ( 8) covalent geometry : bond 0.00298 ( 6701) covalent geometry : angle 0.73187 ( 9098) Misc. bond : bond 0.00025 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.777 Fit side-chains REVERT: A 111 MET cc_start: 0.8132 (ttt) cc_final: 0.7826 (ttt) REVERT: A 112 MET cc_start: 0.7760 (ttm) cc_final: 0.7439 (tmm) REVERT: D 22 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8626 (tt0) REVERT: D 108 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8515 (tm-30) REVERT: D 118 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8434 (tptp) REVERT: F 6 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.7012 (mmm160) outliers start: 20 outliers final: 9 residues processed: 62 average time/residue: 1.5431 time to fit residues: 100.4720 Evaluate side-chains 55 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain F residue 6 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 70 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 61 optimal weight: 50.0000 chunk 82 optimal weight: 40.0000 chunk 74 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 59 optimal weight: 20.0000 chunk 3 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.073510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.050012 restraints weight = 47565.692| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 4.79 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6712 Z= 0.167 Angle : 0.757 41.838 9109 Z= 0.341 Chirality : 0.041 0.187 1063 Planarity : 0.003 0.049 1144 Dihedral : 8.361 81.866 1088 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.93 % Favored : 95.96 % Rotamer: Outliers : 3.75 % Allowed : 25.09 % Favored : 71.16 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.29), residues: 893 helix: 3.09 (0.26), residues: 404 sheet: 1.40 (0.38), residues: 208 loop : -0.84 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 69 HIS 0.004 0.001 HIS A 535 PHE 0.012 0.001 PHE A 308 TYR 0.008 0.001 TYR C 160 ARG 0.005 0.000 ARG F 6 Details of bonding type rmsd link_TRANS : bond 0.00042 ( 1) link_TRANS : angle 0.31608 ( 3) hydrogen bonds : bond 0.06849 ( 428) hydrogen bonds : angle 4.10385 ( 1239) SS BOND : bond 0.00385 ( 4) SS BOND : angle 0.77619 ( 8) covalent geometry : bond 0.00372 ( 6701) covalent geometry : angle 0.75708 ( 9098) Misc. bond : bond 0.00030 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 47 time to evaluate : 0.796 Fit side-chains REVERT: A 111 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7901 (ttt) REVERT: A 112 MET cc_start: 0.7723 (ttm) cc_final: 0.7402 (tmm) REVERT: D 22 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8620 (tt0) REVERT: D 108 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8516 (tm-30) outliers start: 22 outliers final: 11 residues processed: 64 average time/residue: 2.1200 time to fit residues: 142.2411 Evaluate side-chains 58 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 80 optimal weight: 50.0000 chunk 73 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 = 0.3499 r_free = 0.3499 target = 0.072064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.048036 restraints weight = 51912.200| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 4.96 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2822 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2822 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6712 Z= 0.216 Angle : 0.781 41.847 9109 Z= 0.361 Chirality : 0.042 0.188 1063 Planarity : 0.004 0.048 1144 Dihedral : 8.464 79.332 1088 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.04 % Favored : 95.84 % Rotamer: Outliers : 3.75 % Allowed : 25.09 % Favored : 71.16 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.29), residues: 893 helix: 2.99 (0.26), residues: 402 sheet: 1.36 (0.38), residues: 214 loop : -0.82 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 69 HIS 0.005 0.001 HIS A 535 PHE 0.012 0.001 PHE A 459 TYR 0.010 0.001 TYR C 160 ARG 0.003 0.000 ARG F 8 Details of bonding type rmsd link_TRANS : bond 0.00080 ( 1) link_TRANS : angle 0.52068 ( 3) hydrogen bonds : bond 0.07894 ( 428) hydrogen bonds : angle 4.28693 ( 1239) SS BOND : bond 0.00341 ( 4) SS BOND : angle 0.90459 ( 8) covalent geometry : bond 0.00497 ( 6701) covalent geometry : angle 0.78138 ( 9098) Misc. bond : bond 0.00033 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 47 time to evaluate : 0.585 Fit side-chains REVERT: A 111 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7937 (ttt) REVERT: A 112 MET cc_start: 0.7786 (ttm) cc_final: 0.7395 (tmm) REVERT: A 198 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.8084 (t80) REVERT: D 22 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8619 (tt0) REVERT: D 108 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8535 (tm-30) REVERT: F 6 ARG cc_start: 0.7612 (mmm160) cc_final: 0.7239 (mmm160) outliers start: 22 outliers final: 13 residues processed: 62 average time/residue: 1.5928 time to fit residues: 104.0087 Evaluate side-chains 60 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 6 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 65 optimal weight: 20.0000 chunk 64 optimal weight: 30.0000 chunk 39 optimal weight: 0.1980 overall best weight: 2.4386 ------------------------------------------------------------------------------- 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 = 0.3518 r_free = 0.3518 target = 0.073026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.049380 restraints weight = 50327.400| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 4.92 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6712 Z= 0.172 Angle : 0.764 41.864 9109 Z= 0.348 Chirality : 0.042 0.199 1063 Planarity : 0.003 0.049 1144 Dihedral : 8.334 78.161 1088 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.93 % Favored : 95.96 % Rotamer: Outliers : 3.41 % Allowed : 26.11 % Favored : 70.48 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.29), residues: 893 helix: 3.01 (0.26), residues: 403 sheet: 1.34 (0.38), residues: 208 loop : -0.84 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 69 HIS 0.004 0.001 HIS A 535 PHE 0.010 0.001 PHE A 308 TYR 0.008 0.001 TYR C 160 ARG 0.004 0.000 ARG F 6 Details of bonding type rmsd link_TRANS : bond 0.00027 ( 1) link_TRANS : angle 0.39685 ( 3) hydrogen bonds : bond 0.07032 ( 428) hydrogen bonds : angle 4.12205 ( 1239) SS BOND : bond 0.00342 ( 4) SS BOND : angle 0.73579 ( 8) covalent geometry : bond 0.00384 ( 6701) covalent geometry : angle 0.76370 ( 9098) Misc. bond : bond 0.00027 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 0.775 Fit side-chains REVERT: A 112 MET cc_start: 0.7711 (ttm) cc_final: 0.7364 (tmm) REVERT: D 22 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8613 (tt0) REVERT: D 108 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8545 (tm-30) REVERT: F 6 ARG cc_start: 0.7616 (mmm160) cc_final: 0.7339 (mmm160) outliers start: 20 outliers final: 13 residues processed: 62 average time/residue: 2.3018 time to fit residues: 150.0047 Evaluate side-chains 59 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 20 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.074557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.050917 restraints weight = 44061.002| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 4.66 r_work: 0.2736 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2728 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2728 r_free = 0.2728 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2728 r_free = 0.2728 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2728 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6712 Z= 0.136 Angle : 0.751 41.870 9109 Z= 0.338 Chirality : 0.041 0.215 1063 Planarity : 0.003 0.049 1144 Dihedral : 8.116 78.474 1087 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.48 % Favored : 96.40 % Rotamer: Outliers : 2.56 % Allowed : 27.13 % Favored : 70.31 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.30), residues: 893 helix: 3.15 (0.26), residues: 403 sheet: 1.42 (0.38), residues: 208 loop : -0.81 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 69 HIS 0.004 0.001 HIS A 535 PHE 0.010 0.001 PHE A 308 TYR 0.007 0.001 TYR C 111 ARG 0.002 0.000 ARG F 8 Details of bonding type rmsd link_TRANS : bond 0.00000 ( 1) link_TRANS : angle 0.44172 ( 3) hydrogen bonds : bond 0.06038 ( 428) hydrogen bonds : angle 3.94921 ( 1239) SS BOND : bond 0.00304 ( 4) SS BOND : angle 0.63996 ( 8) covalent geometry : bond 0.00288 ( 6701) covalent geometry : angle 0.75159 ( 9098) Misc. bond : bond 0.00026 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.776 Fit side-chains REVERT: D 22 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8738 (tt0) REVERT: D 108 GLU cc_start: 0.9144 (tm-30) cc_final: 0.8768 (tm-30) outliers start: 15 outliers final: 10 residues processed: 59 average time/residue: 1.6032 time to fit residues: 99.6723 Evaluate side-chains 57 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 60 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 62 optimal weight: 30.0000 chunk 74 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 23 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.076344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.052838 restraints weight = 53215.652| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 5.13 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6712 Z= 0.122 Angle : 0.771 41.870 9109 Z= 0.341 Chirality : 0.041 0.226 1063 Planarity : 0.003 0.049 1144 Dihedral : 7.949 79.200 1087 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.37 % Favored : 96.52 % Rotamer: Outliers : 1.71 % Allowed : 28.67 % Favored : 69.62 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.30), residues: 893 helix: 3.21 (0.26), residues: 403 sheet: 1.46 (0.38), residues: 208 loop : -0.77 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 69 HIS 0.003 0.001 HIS A 535 PHE 0.011 0.001 PHE A 114 TYR 0.007 0.001 TYR C 111 ARG 0.002 0.000 ARG A 88 Details of bonding type rmsd link_TRANS : bond 0.00009 ( 1) link_TRANS : angle 0.48703 ( 3) hydrogen bonds : bond 0.05178 ( 428) hydrogen bonds : angle 3.79664 ( 1239) SS BOND : bond 0.00280 ( 4) SS BOND : angle 0.62340 ( 8) covalent geometry : bond 0.00251 ( 6701) covalent geometry : angle 0.77107 ( 9098) Misc. bond : bond 0.00030 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.668 Fit side-chains REVERT: C 125 GLU cc_start: 0.6703 (tp30) cc_final: 0.6384 (tp30) REVERT: D 20 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8212 (tm-30) REVERT: D 108 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8553 (tm-30) outliers start: 10 outliers final: 9 residues processed: 58 average time/residue: 1.4082 time to fit residues: 85.8275 Evaluate side-chains 55 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain D residue 136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 61 optimal weight: 50.0000 chunk 4 optimal weight: 0.0370 chunk 83 optimal weight: 0.2980 chunk 47 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 81 optimal weight: 30.0000 chunk 1 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- 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 = 0.3594 r_free = 0.3594 target = 0.076800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.053432 restraints weight = 61113.060| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 5.54 r_work: 0.2802 rms_B_bonded: 5.53 restraints_weight: 2.0000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 6712 Z= 0.118 Angle : 0.760 41.868 9109 Z= 0.334 Chirality : 0.040 0.240 1063 Planarity : 0.003 0.050 1144 Dihedral : 7.769 79.647 1086 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.48 % Favored : 96.40 % Rotamer: Outliers : 1.37 % Allowed : 28.84 % Favored : 69.80 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.30), residues: 893 helix: 3.27 (0.26), residues: 403 sheet: 1.28 (0.38), residues: 216 loop : -0.72 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 69 HIS 0.003 0.001 HIS A 535 PHE 0.010 0.001 PHE A 295 TYR 0.006 0.001 TYR C 111 ARG 0.002 0.000 ARG A 88 Details of bonding type rmsd link_TRANS : bond 0.00041 ( 1) link_TRANS : angle 0.47503 ( 3) hydrogen bonds : bond 0.04794 ( 428) hydrogen bonds : angle 3.70921 ( 1239) SS BOND : bond 0.00267 ( 4) SS BOND : angle 0.59497 ( 8) covalent geometry : bond 0.00243 ( 6701) covalent geometry : angle 0.76009 ( 9098) Misc. bond : bond 0.00027 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5079.09 seconds wall clock time: 91 minutes 26.74 seconds (5486.74 seconds total)