Starting phenix.real_space_refine on Wed Aug 5 00:21:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k69_36919/08_2026/8k69_36919.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k69_36919/08_2026/8k69_36919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k69_36919/08_2026/8k69_36919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k69_36919/08_2026/8k69_36919.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k69_36919/08_2026/8k69_36919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k69_36919/08_2026/8k69_36919.map" } resolution = 2.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 36 5.16 5 Na 6 4.78 5 C 5140 2.51 5 N 1140 2.21 5 O 1416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7744 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3577 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 458, 3574 Classifications: {'peptide': 458} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 440} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 458, 3574 Classifications: {'peptide': 458} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 440} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 3657 Chain: "B" Number of atoms: 3577 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 458, 3574 Classifications: {'peptide': 458} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 440} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 458, 3574 Classifications: {'peptide': 458} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 440} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 3657 Chain: "A" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 232 Unusual residues: {' NA': 3, 'CLR': 1, 'PC1': 1, 'PTY': 1, 'T7X': 1, 'Y01': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'T7X:plan-5': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 232 Unusual residues: {' NA': 3, 'CLR': 1, 'PC1': 1, 'PTY': 1, 'T7X': 1, 'Y01': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'T7X:plan-5': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Time building chain proxies: 2.34, per 1000 atoms: 0.30 Number of scatterers: 7744 At special positions: 0 Unit cell: (86.7227, 107.191, 84.0294, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 6 15.00 Na 6 11.00 O 1416 8.00 N 1140 7.00 C 5140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG ACYS A 488 " distance=2.08 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG ACYS B 488 " distance=2.08 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 Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 323.1 milliseconds 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1716 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 2 sheets defined 77.4% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 22 through 38 Processing helix chain 'A' and resid 39 through 62 Processing helix chain 'A' and resid 72 through 85 Processing helix chain 'A' and resid 93 through 97 removed outlier: 3.543A pdb=" N VAL A 96 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 113 Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 179 through 214 Processing helix chain 'A' and resid 214 through 225 Proline residue: A 220 - end of helix Processing helix chain 'A' and resid 227 through 242 Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 258 through 273 Processing helix chain 'A' and resid 275 through 292 Processing helix chain 'A' and resid 293 through 301 Processing helix chain 'A' and resid 313 through 340 Processing helix chain 'A' and resid 342 through 346 Processing helix chain 'A' and resid 349 through 364 Processing helix chain 'A' and resid 373 through 377 Processing helix chain 'A' and resid 378 through 391 removed outlier: 3.537A pdb=" N LEU A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 423 Processing helix chain 'A' and resid 425 through 441 Processing helix chain 'A' and resid 441 through 448 Processing helix chain 'A' and resid 453 through 467 Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.714A pdb=" N LEU A 479 " --> pdb=" O SER A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 500 through 516 Processing helix chain 'A' and resid 516 through 521 removed outlier: 3.583A pdb=" N THR A 520 " --> pdb=" O LEU A 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 38 Processing helix chain 'B' and resid 39 through 62 Processing helix chain 'B' and resid 72 through 85 Processing helix chain 'B' and resid 93 through 97 removed outlier: 3.543A pdb=" N VAL B 96 " --> pdb=" O GLU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 113 Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 179 through 214 Processing helix chain 'B' and resid 214 through 225 Proline residue: B 220 - end of helix Processing helix chain 'B' and resid 227 through 242 Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 258 through 273 Processing helix chain 'B' and resid 275 through 292 Processing helix chain 'B' and resid 293 through 301 Processing helix chain 'B' and resid 313 through 340 Processing helix chain 'B' and resid 342 through 346 Processing helix chain 'B' and resid 349 through 364 Processing helix chain 'B' and resid 373 through 377 Processing helix chain 'B' and resid 378 through 391 removed outlier: 3.537A pdb=" N LEU B 384 " --> pdb=" O ALA B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 423 Processing helix chain 'B' and resid 425 through 441 Processing helix chain 'B' and resid 441 through 448 Processing helix chain 'B' and resid 453 through 467 Processing helix chain 'B' and resid 475 through 481 removed outlier: 3.714A pdb=" N LEU B 479 " --> pdb=" O SER B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'B' and resid 500 through 516 Processing helix chain 'B' and resid 516 through 521 removed outlier: 3.582A pdb=" N THR B 520 " --> pdb=" O LEU B 516 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 396 through 397 Processing sheet with id=AA2, first strand: chain 'A' and resid 527 through 528 501 hydrogen bonds defined for protein. 1437 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.96 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1105 1.32 - 1.44: 2053 1.44 - 1.57: 4570 1.57 - 1.69: 12 1.69 - 1.82: 62 Bond restraints: 7802 Sorted by residual: bond pdb=" N ILE A 92 " pdb=" CA ILE A 92 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.11e-02 8.12e+03 1.21e+01 bond pdb=" N ILE B 92 " pdb=" CA ILE B 92 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.11e-02 8.12e+03 1.21e+01 bond pdb=" N CYS A 476 " pdb=" CA CYS A 476 " ideal model delta sigma weight residual 1.459 1.501 -0.041 1.21e-02 6.83e+03 1.18e+01 bond pdb=" N CYS B 476 " pdb=" CA CYS B 476 " ideal model delta sigma weight residual 1.459 1.501 -0.041 1.21e-02 6.83e+03 1.18e+01 bond pdb=" N VAL A 86 " pdb=" CA VAL A 86 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.89e+00 ... (remaining 7797 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 9935 1.90 - 3.81: 573 3.81 - 5.71: 66 5.71 - 7.62: 12 7.62 - 9.52: 4 Bond angle restraints: 10590 Sorted by residual: angle pdb=" C CYS A 476 " pdb=" CA CYS A 476 " pdb=" CB CYS A 476 " ideal model delta sigma weight residual 110.79 102.52 8.27 1.66e+00 3.63e-01 2.48e+01 angle pdb=" C CYS B 476 " pdb=" CA CYS B 476 " pdb=" CB CYS B 476 " ideal model delta sigma weight residual 110.79 102.52 8.27 1.66e+00 3.63e-01 2.48e+01 angle pdb=" C LYS B 409 " pdb=" CA LYS B 409 " pdb=" CB LYS B 409 " ideal model delta sigma weight residual 116.63 111.03 5.60 1.16e+00 7.43e-01 2.33e+01 angle pdb=" C LYS A 409 " pdb=" CA LYS A 409 " pdb=" CB LYS A 409 " ideal model delta sigma weight residual 116.63 111.03 5.60 1.16e+00 7.43e-01 2.33e+01 angle pdb=" N SER B 87 " pdb=" CA SER B 87 " pdb=" C SER B 87 " ideal model delta sigma weight residual 112.04 106.52 5.52 1.44e+00 4.82e-01 1.47e+01 ... (remaining 10585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.38: 4516 26.38 - 52.76: 311 52.76 - 79.14: 55 79.14 - 105.52: 6 105.52 - 131.90: 2 Dihedral angle restraints: 4890 sinusoidal: 2226 harmonic: 2664 Sorted by residual: dihedral pdb=" C3 PTY B 705 " pdb=" O11 PTY B 705 " pdb=" P1 PTY B 705 " pdb=" O12 PTY B 705 " ideal model delta sinusoidal sigma weight residual -59.77 72.13 -131.90 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" C3 PTY A 604 " pdb=" O11 PTY A 604 " pdb=" P1 PTY A 604 " pdb=" O12 PTY A 604 " ideal model delta sinusoidal sigma weight residual -59.77 72.11 -131.88 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" CA MET A 123 " pdb=" C MET A 123 " pdb=" N LEU A 124 " pdb=" CA LEU A 124 " ideal model delta harmonic sigma weight residual -180.00 -160.75 -19.25 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 4887 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1016 0.063 - 0.127: 197 0.127 - 0.190: 27 0.190 - 0.253: 12 0.253 - 0.316: 2 Chirality restraints: 1254 Sorted by residual: chirality pdb=" CBG Y01 B 702 " pdb=" CAQ Y01 B 702 " pdb=" CBD Y01 B 702 " pdb=" CBI Y01 B 702 " both_signs ideal model delta sigma weight residual False -2.33 -2.65 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CBG Y01 A 601 " pdb=" CAQ Y01 A 601 " pdb=" CBD Y01 A 601 " pdb=" CBI Y01 A 601 " both_signs ideal model delta sigma weight residual False -2.33 -2.65 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CBF Y01 A 601 " pdb=" CAS Y01 A 601 " pdb=" CBD Y01 A 601 " pdb=" CBH Y01 A 601 " both_signs ideal model delta sigma weight residual False -2.45 -2.70 0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 1251 not shown) Planarity restraints: 1222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 T7X B 704 " 0.219 2.00e-02 2.50e+03 2.19e-01 4.81e+02 pdb=" C18 T7X B 704 " -0.220 2.00e-02 2.50e+03 pdb=" C19 T7X B 704 " -0.219 2.00e-02 2.50e+03 pdb=" C20 T7X B 704 " 0.219 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 T7X A 603 " 0.219 2.00e-02 2.50e+03 2.19e-01 4.80e+02 pdb=" C18 T7X A 603 " -0.219 2.00e-02 2.50e+03 pdb=" C19 T7X A 603 " -0.219 2.00e-02 2.50e+03 pdb=" C20 T7X A 603 " 0.219 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C14 T7X B 704 " 0.072 2.00e-02 2.50e+03 1.39e-01 1.94e+02 pdb=" C15 T7X B 704 " -0.183 2.00e-02 2.50e+03 pdb=" C16 T7X B 704 " 0.183 2.00e-02 2.50e+03 pdb=" C17 T7X B 704 " -0.072 2.00e-02 2.50e+03 ... (remaining 1219 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 96 2.61 - 3.18: 6733 3.18 - 3.76: 12788 3.76 - 4.33: 18580 4.33 - 4.90: 28343 Nonbonded interactions: 66540 Sorted by model distance: nonbonded pdb=" O HOH B 825 " pdb=" O HOH B 832 " model vdw 2.040 3.040 nonbonded pdb=" O ASN B 467 " pdb=" O HOH B 801 " model vdw 2.082 3.040 nonbonded pdb=" O ASN A 467 " pdb=" O HOH A 701 " model vdw 2.082 3.040 nonbonded pdb="NA NA B 708 " pdb=" O HOH B 801 " model vdw 2.100 2.470 nonbonded pdb="NA NA A 607 " pdb=" O HOH A 701 " model vdw 2.100 2.470 ... (remaining 66535 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 487 or resid 489 through 530 or resid 602 or re \ sid 607 through 609)) selection = (chain 'B' and (resid 22 through 487 or resid 489 through 530 or resid 702 or re \ sid 707 through 709)) } 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=0.50 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: 8.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.520 Find NCS groups from input model: 0.090 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:5.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 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 : 0.007 0.057 7804 Z= 0.447 Angle : 0.977 16.374 10594 Z= 0.590 Chirality : 0.057 0.316 1254 Planarity : 0.012 0.219 1222 Dihedral : 17.308 131.899 3168 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.86 % Favored : 96.92 % Rotamer: Outliers : 5.85 % Allowed : 8.78 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.25), residues: 910 helix: 0.65 (0.19), residues: 642 sheet: None (None), residues: 0 loop : -0.69 (0.34), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 32 TYR 0.019 0.002 TYR B 195 PHE 0.011 0.002 PHE A 196 TRP 0.010 0.002 TRP B 527 HIS 0.004 0.002 HIS B 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00731 / 0.44 ( 7802) covalent geometry : angle 0.93915 / 0.58 (10590) SS BOND : bond 0.05149 / 2.58 ( 2) SS BOND : angle 13.83437 / 8.35 ( 4) hydrogen bonds : bond 0.12889 / 8.90 ( 501) hydrogen bonds : angle 4.63346 / 3.44 ( 1437) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 124 time to evaluate : 0.186 Fit side-chains REVERT: A 63 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.6718 (tmtm) REVERT: A 125 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7374 (ptm160) REVERT: A 414 LYS cc_start: 0.5785 (OUTLIER) cc_final: 0.4874 (tmtm) REVERT: A 415 LEU cc_start: 0.6724 (OUTLIER) cc_final: 0.6355 (tm) REVERT: A 442 ARG cc_start: 0.7155 (ptt-90) cc_final: 0.5915 (ptm160) REVERT: A 478 ARG cc_start: 0.7262 (mtm-85) cc_final: 0.6498 (mtm-85) REVERT: A 480 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7068 (mt0) REVERT: A 525 GLU cc_start: 0.7474 (tp30) cc_final: 0.7187 (tp30) REVERT: B 63 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.6720 (tmtm) REVERT: B 125 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7372 (ptm160) REVERT: B 414 LYS cc_start: 0.5790 (OUTLIER) cc_final: 0.4874 (tmtm) REVERT: B 415 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.6352 (tm) REVERT: B 442 ARG cc_start: 0.7153 (ptt-90) cc_final: 0.5914 (ptm160) REVERT: B 478 ARG cc_start: 0.7247 (mtm-85) cc_final: 0.6496 (mtm-85) REVERT: B 480 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7071 (mt0) REVERT: B 525 GLU cc_start: 0.7471 (tp30) cc_final: 0.7183 (tp30) outliers start: 44 outliers final: 14 residues processed: 152 average time/residue: 0.4801 time to fit residues: 76.8682 Evaluate side-chains 145 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 414 LYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 125 ARG Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 414 LYS Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 480 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 0.3980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 50.0000 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 0.0980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 200 HIS A 251 ASN A 421 ASN B 39 HIS B 200 HIS B 251 ASN B 421 ASN B 483 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.130874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.095408 restraints weight = 9700.957| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 1.33 r_work: 0.2794 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9024 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7804 Z= 0.113 Angle : 0.530 4.859 10594 Z= 0.277 Chirality : 0.038 0.125 1254 Planarity : 0.004 0.041 1222 Dihedral : 14.198 105.113 1630 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.93 % Allowed : 11.70 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.27), residues: 910 helix: 2.09 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.54 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 32 TYR 0.015 0.002 TYR A 195 PHE 0.009 0.001 PHE A 196 TRP 0.010 0.001 TRP B 186 HIS 0.002 0.001 HIS A 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 ( 7802) covalent geometry : angle 0.52451 / 0.27 (10590) SS BOND : bond 0.00885 / 0.44 ( 2) SS BOND : angle 3.79139 / 2.32 ( 4) hydrogen bonds : bond 0.04234 / 2.85 ( 501) hydrogen bonds : angle 3.97862 / 2.97 ( 1437) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.243 Fit side-chains REVERT: A 414 LYS cc_start: 0.6365 (OUTLIER) cc_final: 0.5383 (tmtm) REVERT: A 415 LEU cc_start: 0.6833 (OUTLIER) cc_final: 0.6545 (tm) REVERT: A 442 ARG cc_start: 0.8702 (ptt-90) cc_final: 0.7983 (ptm160) REVERT: A 478 ARG cc_start: 0.8502 (mtm-85) cc_final: 0.8068 (mtm-85) REVERT: A 480 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8018 (mt0) REVERT: A 489 GLN cc_start: 0.7170 (mm-40) cc_final: 0.6962 (mm-40) REVERT: B 414 LYS cc_start: 0.6387 (OUTLIER) cc_final: 0.5403 (tmtm) REVERT: B 415 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6522 (tm) REVERT: B 442 ARG cc_start: 0.8709 (ptt-90) cc_final: 0.7988 (ptm160) REVERT: B 478 ARG cc_start: 0.8508 (mtm-85) cc_final: 0.8073 (mtm-85) REVERT: B 480 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8030 (mt0) REVERT: B 489 GLN cc_start: 0.7177 (mm-40) cc_final: 0.6968 (mm-40) outliers start: 23 outliers final: 4 residues processed: 135 average time/residue: 0.5216 time to fit residues: 73.8791 Evaluate side-chains 129 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 414 LYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 414 LYS Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 480 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 50 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 chunk 2 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 483 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.129263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.094583 restraints weight = 9270.852| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 1.28 r_work: 0.2782 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2654 r_free = 0.2654 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2654 r_free = 0.2654 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9042 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7804 Z= 0.125 Angle : 0.550 4.992 10594 Z= 0.286 Chirality : 0.039 0.128 1254 Planarity : 0.004 0.040 1222 Dihedral : 12.971 95.645 1600 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.80 % Allowed : 12.21 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.27), residues: 910 helix: 2.31 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.53 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 32 TYR 0.017 0.002 TYR B 73 PHE 0.012 0.001 PHE A 196 TRP 0.006 0.001 TRP B 186 HIS 0.002 0.001 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 ( 7802) covalent geometry : angle 0.54663 / 0.28 (10590) SS BOND : bond 0.01032 / 0.52 ( 2) SS BOND : angle 3.23929 / 1.96 ( 4) hydrogen bonds : bond 0.04652 / 3.13 ( 501) hydrogen bonds : angle 3.95596 / 2.96 ( 1437) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.186 Fit side-chains REVERT: A 49 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8321 (tt) REVERT: A 61 PHE cc_start: 0.7814 (m-10) cc_final: 0.7261 (t80) REVERT: A 179 LYS cc_start: 0.5927 (OUTLIER) cc_final: 0.5124 (mmpt) REVERT: A 414 LYS cc_start: 0.6568 (OUTLIER) cc_final: 0.5548 (tmtm) REVERT: A 415 LEU cc_start: 0.6948 (OUTLIER) cc_final: 0.6549 (tm) REVERT: A 442 ARG cc_start: 0.8694 (ptt-90) cc_final: 0.7982 (ptm160) REVERT: A 478 ARG cc_start: 0.8511 (mtm-85) cc_final: 0.8157 (mtm-85) REVERT: A 489 GLN cc_start: 0.7223 (mm-40) cc_final: 0.7005 (mm-40) REVERT: B 49 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8324 (tt) REVERT: B 61 PHE cc_start: 0.7813 (m-10) cc_final: 0.7256 (t80) REVERT: B 179 LYS cc_start: 0.5931 (OUTLIER) cc_final: 0.5128 (mmpt) REVERT: B 414 LYS cc_start: 0.6574 (OUTLIER) cc_final: 0.5560 (tmtm) REVERT: B 415 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6560 (tm) REVERT: B 442 ARG cc_start: 0.8691 (ptt-90) cc_final: 0.7980 (ptm160) REVERT: B 478 ARG cc_start: 0.8511 (mtm-85) cc_final: 0.8162 (mtm-85) REVERT: B 489 GLN cc_start: 0.7232 (mm-40) cc_final: 0.7021 (mm-40) outliers start: 22 outliers final: 6 residues processed: 127 average time/residue: 0.5370 time to fit residues: 71.5802 Evaluate side-chains 128 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 414 LYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 414 LYS Chi-restraints excluded: chain B residue 415 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.125977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.090271 restraints weight = 8325.382| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 1.29 r_work: 0.2729 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2606 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.2606 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7804 Z= 0.193 Angle : 0.669 5.609 10594 Z= 0.342 Chirality : 0.044 0.151 1254 Planarity : 0.005 0.048 1222 Dihedral : 13.545 90.300 1594 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.16 % Allowed : 12.98 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.27), residues: 910 helix: 2.06 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.47 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 32 TYR 0.022 0.003 TYR B 73 PHE 0.013 0.002 PHE A 459 TRP 0.009 0.002 TRP A 498 HIS 0.003 0.002 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 ( 7802) covalent geometry : angle 0.66590 / 0.34 (10590) SS BOND : bond 0.00736 / 0.37 ( 2) SS BOND : angle 3.19544 / 1.91 ( 4) hydrogen bonds : bond 0.05871 / 3.96 ( 501) hydrogen bonds : angle 4.13736 / 3.09 ( 1437) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.187 Fit side-chains REVERT: A 49 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8362 (tt) REVERT: A 179 LYS cc_start: 0.5979 (OUTLIER) cc_final: 0.5559 (pptt) REVERT: A 414 LYS cc_start: 0.6622 (OUTLIER) cc_final: 0.5615 (tmtm) REVERT: A 442 ARG cc_start: 0.8693 (ptt-90) cc_final: 0.7932 (ptm160) REVERT: A 478 ARG cc_start: 0.8456 (mtm-85) cc_final: 0.8028 (mtm-85) REVERT: A 489 GLN cc_start: 0.7259 (mm-40) cc_final: 0.6989 (mm-40) REVERT: B 49 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8363 (tt) REVERT: B 179 LYS cc_start: 0.5983 (OUTLIER) cc_final: 0.5562 (pptt) REVERT: B 414 LYS cc_start: 0.6629 (OUTLIER) cc_final: 0.5621 (tmtm) REVERT: B 442 ARG cc_start: 0.8694 (ptt-90) cc_final: 0.7930 (ptm160) REVERT: B 478 ARG cc_start: 0.8451 (mtm-85) cc_final: 0.8024 (mtm-85) REVERT: B 489 GLN cc_start: 0.7272 (mm-40) cc_final: 0.7006 (mm-40) outliers start: 17 outliers final: 8 residues processed: 117 average time/residue: 0.5838 time to fit residues: 71.5888 Evaluate side-chains 124 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 414 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 414 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 52 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.128689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.093232 restraints weight = 7973.478| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 1.33 r_work: 0.2782 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7804 Z= 0.123 Angle : 0.544 4.996 10594 Z= 0.283 Chirality : 0.038 0.129 1254 Planarity : 0.004 0.040 1222 Dihedral : 12.535 84.670 1590 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.42 % Allowed : 12.85 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.27), residues: 910 helix: 2.41 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.46 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 32 TYR 0.016 0.002 TYR A 73 PHE 0.012 0.001 PHE B 196 TRP 0.008 0.001 TRP A 186 HIS 0.002 0.001 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 7802) covalent geometry : angle 0.54149 / 0.28 (10590) SS BOND : bond 0.00959 / 0.48 ( 2) SS BOND : angle 2.69930 / 1.63 ( 4) hydrogen bonds : bond 0.04504 / 3.03 ( 501) hydrogen bonds : angle 3.94223 / 2.95 ( 1437) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.297 Fit side-chains REVERT: A 49 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8258 (tt) REVERT: A 61 PHE cc_start: 0.7718 (m-10) cc_final: 0.7085 (t80) REVERT: A 179 LYS cc_start: 0.5923 (OUTLIER) cc_final: 0.5572 (pmtt) REVERT: A 442 ARG cc_start: 0.8606 (ptt-90) cc_final: 0.7809 (ptm160) REVERT: A 478 ARG cc_start: 0.8412 (mtm-85) cc_final: 0.7992 (mtm-85) REVERT: A 489 GLN cc_start: 0.7138 (OUTLIER) cc_final: 0.6889 (mm-40) REVERT: B 49 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8255 (tt) REVERT: B 61 PHE cc_start: 0.7710 (m-10) cc_final: 0.7082 (t80) REVERT: B 179 LYS cc_start: 0.5919 (OUTLIER) cc_final: 0.5575 (pmtt) REVERT: B 442 ARG cc_start: 0.8609 (ptt-90) cc_final: 0.7805 (ptm160) REVERT: B 478 ARG cc_start: 0.8405 (mtm-85) cc_final: 0.7986 (mtm-85) REVERT: B 489 GLN cc_start: 0.7145 (OUTLIER) cc_final: 0.6891 (mm-40) outliers start: 17 outliers final: 7 residues processed: 118 average time/residue: 0.6013 time to fit residues: 74.4433 Evaluate side-chains 127 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 489 GLN Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 489 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 39 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 33 optimal weight: 50.0000 chunk 1 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.128267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.092109 restraints weight = 9217.371| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 1.38 r_work: 0.2765 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2641 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7804 Z= 0.132 Angle : 0.561 5.309 10594 Z= 0.291 Chirality : 0.039 0.132 1254 Planarity : 0.004 0.040 1222 Dihedral : 12.158 80.365 1582 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.04 % Allowed : 13.23 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.27), residues: 910 helix: 2.41 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.47 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 32 TYR 0.018 0.002 TYR B 73 PHE 0.012 0.001 PHE A 196 TRP 0.006 0.001 TRP A 186 HIS 0.003 0.001 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 7802) covalent geometry : angle 0.55837 / 0.29 (10590) SS BOND : bond 0.00885 / 0.44 ( 2) SS BOND : angle 2.75434 / 1.65 ( 4) hydrogen bonds : bond 0.04751 / 3.20 ( 501) hydrogen bonds : angle 3.96051 / 2.96 ( 1437) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.266 Fit side-chains REVERT: A 49 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8266 (tt) REVERT: A 61 PHE cc_start: 0.7772 (m-10) cc_final: 0.7126 (t80) REVERT: A 179 LYS cc_start: 0.5922 (OUTLIER) cc_final: 0.5573 (pmtt) REVERT: A 442 ARG cc_start: 0.8642 (ptt-90) cc_final: 0.7839 (ptm160) REVERT: A 478 ARG cc_start: 0.8411 (mtm-85) cc_final: 0.7997 (mtp180) REVERT: A 489 GLN cc_start: 0.7156 (OUTLIER) cc_final: 0.6896 (mm-40) REVERT: B 49 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8268 (tt) REVERT: B 61 PHE cc_start: 0.7768 (m-10) cc_final: 0.7123 (t80) REVERT: B 179 LYS cc_start: 0.5925 (OUTLIER) cc_final: 0.5578 (pmtt) REVERT: B 442 ARG cc_start: 0.8643 (ptt-90) cc_final: 0.7834 (ptm160) REVERT: B 478 ARG cc_start: 0.8409 (mtm-85) cc_final: 0.7996 (mtp180) REVERT: B 489 GLN cc_start: 0.7149 (OUTLIER) cc_final: 0.6893 (mm-40) outliers start: 14 outliers final: 4 residues processed: 117 average time/residue: 0.5354 time to fit residues: 65.6766 Evaluate side-chains 123 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 489 GLN Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 489 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 50.0000 chunk 27 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 480 GLN B 480 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.125145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.088802 restraints weight = 9931.023| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 1.43 r_work: 0.2705 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2587 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7804 Z= 0.238 Angle : 0.730 6.286 10594 Z= 0.370 Chirality : 0.048 0.167 1254 Planarity : 0.005 0.061 1222 Dihedral : 13.086 84.898 1578 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.80 % Allowed : 12.60 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.27), residues: 910 helix: 1.91 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.39 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 32 TYR 0.024 0.003 TYR B 73 PHE 0.014 0.002 PHE B 459 TRP 0.010 0.002 TRP A 498 HIS 0.005 0.002 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.24 ( 7802) covalent geometry : angle 0.72765 / 0.37 (10590) SS BOND : bond 0.00693 / 0.35 ( 2) SS BOND : angle 3.08192 / 1.81 ( 4) hydrogen bonds : bond 0.06356 / 4.29 ( 501) hydrogen bonds : angle 4.17789 / 3.12 ( 1437) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.177 Fit side-chains REVERT: A 179 LYS cc_start: 0.5981 (OUTLIER) cc_final: 0.5604 (pmtt) REVERT: A 292 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7801 (mppt) REVERT: A 442 ARG cc_start: 0.8724 (ptt-90) cc_final: 0.7972 (ptm160) REVERT: A 478 ARG cc_start: 0.8470 (mtm-85) cc_final: 0.8011 (mtm-85) REVERT: A 489 GLN cc_start: 0.7337 (OUTLIER) cc_final: 0.7082 (mm-40) REVERT: B 179 LYS cc_start: 0.5983 (OUTLIER) cc_final: 0.5611 (pmtt) REVERT: B 292 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7796 (mppt) REVERT: B 442 ARG cc_start: 0.8722 (ptt-90) cc_final: 0.7968 (ptm160) REVERT: B 478 ARG cc_start: 0.8472 (mtm-85) cc_final: 0.8029 (mtm-85) REVERT: B 489 GLN cc_start: 0.7349 (OUTLIER) cc_final: 0.7093 (mm-40) outliers start: 20 outliers final: 6 residues processed: 118 average time/residue: 0.5424 time to fit residues: 67.0920 Evaluate side-chains 124 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 489 GLN Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 489 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 41 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.128784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.094324 restraints weight = 6785.326| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.22 r_work: 0.2793 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2671 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2671 r_free = 0.2671 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2671 r_free = 0.2671 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2671 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7804 Z= 0.124 Angle : 0.548 4.994 10594 Z= 0.285 Chirality : 0.038 0.130 1254 Planarity : 0.004 0.041 1222 Dihedral : 12.124 80.982 1578 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.29 % Allowed : 13.36 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.27), residues: 910 helix: 2.38 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.44 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 32 TYR 0.017 0.002 TYR B 195 PHE 0.012 0.001 PHE A 196 TRP 0.008 0.001 TRP B 186 HIS 0.002 0.001 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 7802) covalent geometry : angle 0.54555 / 0.28 (10590) SS BOND : bond 0.00906 / 0.45 ( 2) SS BOND : angle 2.63025 / 1.57 ( 4) hydrogen bonds : bond 0.04517 / 3.04 ( 501) hydrogen bonds : angle 3.94112 / 2.94 ( 1437) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.218 Fit side-chains REVERT: A 61 PHE cc_start: 0.7742 (m-10) cc_final: 0.7104 (t80) REVERT: A 179 LYS cc_start: 0.5935 (OUTLIER) cc_final: 0.5592 (pmtt) REVERT: A 442 ARG cc_start: 0.8606 (ptt-90) cc_final: 0.7810 (ptm160) REVERT: A 478 ARG cc_start: 0.8388 (mtm-85) cc_final: 0.7989 (mtp180) REVERT: A 489 GLN cc_start: 0.7144 (OUTLIER) cc_final: 0.6888 (mm-40) REVERT: B 61 PHE cc_start: 0.7738 (m-10) cc_final: 0.7098 (t80) REVERT: B 179 LYS cc_start: 0.5935 (OUTLIER) cc_final: 0.5593 (pmtt) REVERT: B 442 ARG cc_start: 0.8604 (ptt-90) cc_final: 0.7801 (ptm160) REVERT: B 478 ARG cc_start: 0.8388 (mtm-85) cc_final: 0.7989 (mtp180) REVERT: B 489 GLN cc_start: 0.7143 (OUTLIER) cc_final: 0.6885 (mm-40) outliers start: 16 outliers final: 4 residues processed: 115 average time/residue: 0.5769 time to fit residues: 69.4240 Evaluate side-chains 121 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 489 GLN Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 489 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 84 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 72 optimal weight: 0.0770 chunk 7 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.127515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.093074 restraints weight = 6693.176| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 1.20 r_work: 0.2769 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2651 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7804 Z= 0.149 Angle : 0.595 5.415 10594 Z= 0.307 Chirality : 0.041 0.142 1254 Planarity : 0.004 0.041 1222 Dihedral : 12.197 80.894 1578 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.53 % Allowed : 14.12 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.27), residues: 910 helix: 2.30 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.42 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 32 TYR 0.019 0.002 TYR B 73 PHE 0.012 0.002 PHE B 196 TRP 0.007 0.001 TRP A 498 HIS 0.003 0.001 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 ( 7802) covalent geometry : angle 0.59316 / 0.31 (10590) SS BOND : bond 0.00896 / 0.45 ( 2) SS BOND : angle 2.76621 / 1.64 ( 4) hydrogen bonds : bond 0.05088 / 3.43 ( 501) hydrogen bonds : angle 4.00626 / 2.99 ( 1437) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.208 Fit side-chains REVERT: A 49 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8299 (tt) REVERT: A 61 PHE cc_start: 0.7798 (m-10) cc_final: 0.7137 (t80) REVERT: A 179 LYS cc_start: 0.5950 (OUTLIER) cc_final: 0.5598 (pmtt) REVERT: A 442 ARG cc_start: 0.8628 (ptt-90) cc_final: 0.7839 (ptm160) REVERT: A 478 ARG cc_start: 0.8391 (mtm-85) cc_final: 0.7957 (mtm-85) REVERT: A 489 GLN cc_start: 0.7170 (OUTLIER) cc_final: 0.6909 (mm-40) REVERT: B 49 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8298 (tt) REVERT: B 61 PHE cc_start: 0.7794 (m-10) cc_final: 0.7138 (t80) REVERT: B 179 LYS cc_start: 0.5957 (OUTLIER) cc_final: 0.5607 (pmtt) REVERT: B 442 ARG cc_start: 0.8625 (ptt-90) cc_final: 0.7831 (ptm160) REVERT: B 478 ARG cc_start: 0.8393 (mtm-85) cc_final: 0.7963 (mtm-85) REVERT: B 489 GLN cc_start: 0.7171 (OUTLIER) cc_final: 0.6909 (mm-40) outliers start: 10 outliers final: 4 residues processed: 116 average time/residue: 0.6385 time to fit residues: 77.5897 Evaluate side-chains 124 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 489 GLN Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 489 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 64 optimal weight: 1.9990 chunk 33 optimal weight: 50.0000 chunk 30 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.127429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.092261 restraints weight = 7443.974| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.28 r_work: 0.2760 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7804 Z= 0.154 Angle : 0.607 5.760 10594 Z= 0.312 Chirality : 0.041 0.135 1254 Planarity : 0.004 0.042 1222 Dihedral : 12.103 80.556 1578 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.04 % Allowed : 13.61 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.27), residues: 910 helix: 2.25 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.41 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 32 TYR 0.020 0.002 TYR B 73 PHE 0.012 0.002 PHE A 196 TRP 0.007 0.001 TRP B 527 HIS 0.003 0.001 HIS B 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 7802) covalent geometry : angle 0.60433 / 0.31 (10590) SS BOND : bond 0.00891 / 0.45 ( 2) SS BOND : angle 2.81047 / 1.67 ( 4) hydrogen bonds : bond 0.05207 / 3.51 ( 501) hydrogen bonds : angle 4.02097 / 3.00 ( 1437) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.235 Fit side-chains REVERT: A 49 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8307 (tt) REVERT: A 61 PHE cc_start: 0.7807 (m-10) cc_final: 0.7138 (t80) REVERT: A 179 LYS cc_start: 0.5976 (OUTLIER) cc_final: 0.5621 (pmtt) REVERT: A 292 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7747 (mppt) REVERT: A 442 ARG cc_start: 0.8642 (ptt-90) cc_final: 0.7849 (ptm160) REVERT: A 478 ARG cc_start: 0.8405 (mtm-85) cc_final: 0.7966 (mtm-85) REVERT: A 489 GLN cc_start: 0.7178 (OUTLIER) cc_final: 0.6875 (mm-40) REVERT: B 49 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8307 (tt) REVERT: B 61 PHE cc_start: 0.7804 (m-10) cc_final: 0.7135 (t80) REVERT: B 179 LYS cc_start: 0.5980 (OUTLIER) cc_final: 0.5628 (pmtt) REVERT: B 292 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7742 (mppt) REVERT: B 442 ARG cc_start: 0.8641 (ptt-90) cc_final: 0.7843 (ptm160) REVERT: B 478 ARG cc_start: 0.8407 (mtm-85) cc_final: 0.7970 (mtm-85) REVERT: B 489 GLN cc_start: 0.7181 (OUTLIER) cc_final: 0.6878 (mm-40) outliers start: 14 outliers final: 4 residues processed: 118 average time/residue: 0.5812 time to fit residues: 71.8464 Evaluate side-chains 126 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 489 GLN Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 489 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.129198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.093028 restraints weight = 9115.728| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 1.40 r_work: 0.2784 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7804 Z= 0.119 Angle : 0.539 4.978 10594 Z= 0.281 Chirality : 0.038 0.123 1254 Planarity : 0.004 0.041 1222 Dihedral : 11.656 79.183 1578 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.53 % Allowed : 14.12 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.27), residues: 910 helix: 2.48 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.42 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 32 TYR 0.016 0.002 TYR B 195 PHE 0.012 0.001 PHE A 196 TRP 0.008 0.001 TRP A 186 HIS 0.002 0.001 HIS B 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 ( 7802) covalent geometry : angle 0.53667 / 0.28 (10590) SS BOND : bond 0.00948 / 0.48 ( 2) SS BOND : angle 2.58106 / 1.53 ( 4) hydrogen bonds : bond 0.04406 / 2.96 ( 501) hydrogen bonds : angle 3.91202 / 2.92 ( 1437) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3229.87 seconds wall clock time: 55 minutes 27.85 seconds (3327.85 seconds total)