Starting phenix.real_space_refine on Fri Aug 22 20:33:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k69_36919/08_2025/8k69_36919.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k69_36919/08_2025/8k69_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_2025/8k69_36919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k69_36919/08_2025/8k69_36919.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k69_36919/08_2025/8k69_36919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k69_36919/08_2025/8k69_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 3.56, per 1000 atoms: 0.46 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: 1.06 Conformation dependent library (CDL) restraints added in 564.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.26 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: 1.28 Time building geometry restraints manager: 1.27 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: 4574 26.38 - 52.76: 323 52.76 - 79.14: 57 79.14 - 105.52: 6 105.52 - 131.90: 4 Dihedral angle restraints: 4964 sinusoidal: 2300 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=" C9 T7X A 603 " pdb=" C7 T7X A 603 " pdb=" C8 T7X A 603 " pdb=" O13 T7X A 603 " ideal model delta sinusoidal sigma weight residual 64.16 -173.35 -122.49 1 3.00e+01 1.11e-03 1.64e+01 ... (remaining 4961 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: 9.290 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.550 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:8.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 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 : 17.641 131.899 3242 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 aren 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 covalent geometry : bond 0.00731 ( 7802) covalent geometry : angle 0.93917 (10590) SS BOND : bond 0.05149 ( 2) SS BOND : angle 13.83437 ( 4) hydrogen bonds : bond 0.12889 ( 501) hydrogen bonds : angle 4.63346 ( 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 : 0.315 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: 0.6974 time to fit residues: 111.3593 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 : 0.327 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.130860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.095345 restraints weight = 9706.047| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 1.33 r_work: 0.2796 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.2672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.1255 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 : 0.532 4.884 10594 Z= 0.277 Chirality : 0.038 0.124 1254 Planarity : 0.004 0.041 1222 Dihedral : 15.126 120.185 1704 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.67 % Allowed : 11.96 % 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 aren not related in a simple way. whole: 2.02 (0.27), residues: 910 helix: 2.09 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.55 (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 0.008 0.001 PHE B 196 TRP 0.010 0.001 TRP B 186 HIS 0.002 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 7802) covalent geometry : angle 0.52646 (10590) SS BOND : bond 0.00918 ( 2) SS BOND : angle 3.85184 ( 4) hydrogen bonds : bond 0.04242 ( 501) hydrogen bonds : angle 3.97586 ( 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 145 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.344 Fit side-chains REVERT: A 414 LYS cc_start: 0.6363 (OUTLIER) cc_final: 0.5378 (tmtm) REVERT: A 415 LEU cc_start: 0.6816 (OUTLIER) cc_final: 0.6524 (tm) REVERT: A 442 ARG cc_start: 0.8694 (ptt-90) cc_final: 0.7990 (ptm160) REVERT: A 478 ARG cc_start: 0.8503 (mtm-85) cc_final: 0.8073 (mtm-85) REVERT: A 480 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8030 (mt0) REVERT: A 489 GLN cc_start: 0.7172 (mm-40) cc_final: 0.6962 (mm-40) REVERT: B 414 LYS cc_start: 0.6365 (OUTLIER) cc_final: 0.5387 (tmtm) REVERT: B 415 LEU cc_start: 0.6815 (OUTLIER) cc_final: 0.6508 (tm) REVERT: B 442 ARG cc_start: 0.8699 (ptt-90) cc_final: 0.7993 (ptm160) REVERT: B 478 ARG cc_start: 0.8506 (mtm-85) cc_final: 0.8074 (mtm-85) REVERT: B 480 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8044 (mt0) REVERT: B 489 GLN cc_start: 0.7176 (mm-40) cc_final: 0.6967 (mm-40) outliers start: 21 outliers final: 4 residues processed: 135 average time/residue: 0.7577 time to fit residues: 107.2655 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 : 0.314 ------------------------------------------------------------------------------- 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: 1.9990 chunk 7 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.128019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.092647 restraints weight = 9286.079| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 1.31 r_work: 0.2756 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7804 Z= 0.133 Angle : 0.567 5.087 10594 Z= 0.294 Chirality : 0.039 0.131 1254 Planarity : 0.004 0.041 1222 Dihedral : 14.133 114.710 1674 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.54 % Allowed : 12.21 % Favored : 85.24 % 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 aren not related in a simple way. whole: 2.23 (0.27), residues: 910 helix: 2.27 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.52 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 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 527 HIS 0.003 0.001 HIS A 483 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 7802) covalent geometry : angle 0.56384 (10590) SS BOND : bond 0.00892 ( 2) SS BOND : angle 3.28620 ( 4) hydrogen bonds : bond 0.04857 ( 501) hydrogen bonds : angle 3.98999 ( 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 135 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.342 Fit side-chains REVERT: A 49 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8326 (tt) REVERT: A 61 PHE cc_start: 0.7845 (m-10) cc_final: 0.7291 (t80) REVERT: A 179 LYS cc_start: 0.5938 (OUTLIER) cc_final: 0.5106 (mmpt) REVERT: A 414 LYS cc_start: 0.6586 (OUTLIER) cc_final: 0.5538 (tmtm) REVERT: A 442 ARG cc_start: 0.8723 (ptt-90) cc_final: 0.8003 (ptm160) REVERT: A 478 ARG cc_start: 0.8535 (mtm-85) cc_final: 0.8177 (mtm-85) REVERT: A 489 GLN cc_start: 0.7269 (mm-40) cc_final: 0.7048 (mm-40) REVERT: B 49 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8327 (tt) REVERT: B 61 PHE cc_start: 0.7844 (m-10) cc_final: 0.7284 (t80) REVERT: B 179 LYS cc_start: 0.5936 (OUTLIER) cc_final: 0.5103 (mmpt) REVERT: B 414 LYS cc_start: 0.6598 (OUTLIER) cc_final: 0.5553 (tmtm) REVERT: B 442 ARG cc_start: 0.8724 (ptt-90) cc_final: 0.8002 (ptm160) REVERT: B 478 ARG cc_start: 0.8528 (mtm-85) cc_final: 0.8175 (mtm-85) REVERT: B 489 GLN cc_start: 0.7280 (mm-40) cc_final: 0.7059 (mm-40) outliers start: 20 outliers final: 6 residues processed: 125 average time/residue: 0.7975 time to fit residues: 104.2411 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 : 0.301 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 81 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 1 optimal weight: 0.0470 chunk 7 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.3884 ------------------------------------------------------------------------------- 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 = 0.3352 r_free = 0.3352 target = 0.126736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.091033 restraints weight = 8335.540| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 1.29 r_work: 0.2743 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7804 Z= 0.169 Angle : 0.628 5.470 10594 Z= 0.323 Chirality : 0.042 0.146 1254 Planarity : 0.005 0.042 1222 Dihedral : 14.211 116.724 1664 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.16 % Allowed : 13.23 % 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 aren not related in a simple way. whole: 2.14 (0.27), residues: 910 helix: 2.16 (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 0.003 0.000 ARG A 32 TYR 0.021 0.003 TYR B 73 PHE 0.012 0.002 PHE A 196 TRP 0.008 0.002 TRP A 498 HIS 0.003 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 7802) covalent geometry : angle 0.62515 (10590) SS BOND : bond 0.00780 ( 2) SS BOND : angle 3.06153 ( 4) hydrogen bonds : bond 0.05485 ( 501) hydrogen bonds : angle 4.07968 ( 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 131 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.306 Fit side-chains REVERT: A 49 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8335 (tt) REVERT: A 179 LYS cc_start: 0.5939 (OUTLIER) cc_final: 0.5526 (pptt) REVERT: A 414 LYS cc_start: 0.6563 (OUTLIER) cc_final: 0.5542 (tmtm) REVERT: A 442 ARG cc_start: 0.8675 (ptt-90) cc_final: 0.7902 (ptm160) REVERT: A 478 ARG cc_start: 0.8435 (mtm-85) cc_final: 0.8011 (mtm-85) REVERT: A 489 GLN cc_start: 0.7236 (mm-40) cc_final: 0.6963 (mm-40) REVERT: B 49 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8337 (tt) REVERT: B 179 LYS cc_start: 0.5948 (OUTLIER) cc_final: 0.5533 (pptt) REVERT: B 414 LYS cc_start: 0.6580 (OUTLIER) cc_final: 0.5557 (tmtm) REVERT: B 442 ARG cc_start: 0.8674 (ptt-90) cc_final: 0.7898 (ptm160) REVERT: B 478 ARG cc_start: 0.8430 (mtm-85) cc_final: 0.8009 (mtm-85) REVERT: B 489 GLN cc_start: 0.7245 (mm-40) cc_final: 0.6971 (mm-40) outliers start: 17 outliers final: 8 residues processed: 121 average time/residue: 0.8141 time to fit residues: 103.1865 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 : 0.306 ------------------------------------------------------------------------------- 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: 3.9990 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 47 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 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: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3333 r_free = 0.3333 target = 0.125075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.089563 restraints weight = 7910.979| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 1.32 r_work: 0.2710 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7804 Z= 0.225 Angle : 0.714 5.762 10594 Z= 0.364 Chirality : 0.047 0.157 1254 Planarity : 0.005 0.056 1222 Dihedral : 14.717 118.894 1664 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.67 % Allowed : 12.47 % 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 aren not related in a simple way. whole: 1.86 (0.27), residues: 910 helix: 1.90 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.40 (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 0.013 0.002 PHE A 459 TRP 0.010 0.002 TRP B 498 HIS 0.004 0.002 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00506 ( 7802) covalent geometry : angle 0.71183 (10590) SS BOND : bond 0.00708 ( 2) SS BOND : angle 3.07283 ( 4) hydrogen bonds : bond 0.06257 ( 501) hydrogen bonds : angle 4.18965 ( 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 132 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.329 Fit side-chains REVERT: A 49 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8365 (tt) REVERT: A 61 PHE cc_start: 0.7834 (m-10) cc_final: 0.7188 (t80) REVERT: A 179 LYS cc_start: 0.5985 (OUTLIER) cc_final: 0.5610 (pmtt) REVERT: A 292 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7798 (mppt) REVERT: A 442 ARG cc_start: 0.8690 (ptt-90) cc_final: 0.7942 (ptm160) REVERT: A 478 ARG cc_start: 0.8448 (mtm-85) cc_final: 0.7999 (mtm-85) REVERT: A 480 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8297 (mt0) REVERT: A 489 GLN cc_start: 0.7334 (OUTLIER) cc_final: 0.7078 (mm-40) REVERT: B 49 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8365 (tt) REVERT: B 61 PHE cc_start: 0.7838 (m-10) cc_final: 0.7187 (t80) REVERT: B 179 LYS cc_start: 0.5990 (OUTLIER) cc_final: 0.5620 (pmtt) REVERT: B 292 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7797 (mppt) REVERT: B 415 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6613 (tm) REVERT: B 442 ARG cc_start: 0.8692 (ptt-90) cc_final: 0.7938 (ptm160) REVERT: B 478 ARG cc_start: 0.8445 (mtm-85) cc_final: 0.7997 (mtm-85) REVERT: B 480 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8298 (mt0) REVERT: B 489 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.7081 (mm-40) outliers start: 21 outliers final: 8 residues processed: 116 average time/residue: 0.7916 time to fit residues: 96.0136 Evaluate side-chains 130 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 292 LYS Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 480 GLN 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 292 LYS Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 480 GLN 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: 0.8980 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 58 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 33 optimal weight: 50.0000 chunk 1 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3374 r_free = 0.3374 target = 0.128184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.091782 restraints weight = 9596.712| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 1.41 r_work: 0.2765 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 3.16 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 = 0.40 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 = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7804 Z= 0.128 Angle : 0.557 5.062 10594 Z= 0.289 Chirality : 0.039 0.133 1254 Planarity : 0.004 0.042 1222 Dihedral : 13.861 116.660 1656 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.16 % Allowed : 13.36 % Favored : 84.48 % 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 aren not related in a simple way. whole: 2.34 (0.27), residues: 910 helix: 2.33 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.45 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 32 TYR 0.017 0.002 TYR A 73 PHE 0.012 0.001 PHE A 196 TRP 0.008 0.001 TRP B 186 HIS 0.002 0.001 HIS B 200 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 7802) covalent geometry : angle 0.55491 (10590) SS BOND : bond 0.00965 ( 2) SS BOND : angle 2.56102 ( 4) hydrogen bonds : bond 0.04664 ( 501) hydrogen bonds : angle 3.97122 ( 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 129 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.324 Fit side-chains REVERT: A 49 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8274 (tt) REVERT: A 61 PHE cc_start: 0.7811 (m-10) cc_final: 0.7161 (t80) REVERT: A 179 LYS cc_start: 0.5947 (OUTLIER) cc_final: 0.5582 (pmtt) REVERT: A 415 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6575 (tm) REVERT: A 442 ARG cc_start: 0.8658 (ptt-90) cc_final: 0.7872 (ptm160) REVERT: A 478 ARG cc_start: 0.8469 (mtm-85) cc_final: 0.8055 (mtm-85) REVERT: A 489 GLN cc_start: 0.7195 (OUTLIER) cc_final: 0.6932 (mm-40) REVERT: B 49 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8274 (tt) REVERT: B 61 PHE cc_start: 0.7810 (m-10) cc_final: 0.7159 (t80) REVERT: B 179 LYS cc_start: 0.5952 (OUTLIER) cc_final: 0.5591 (pmtt) REVERT: B 442 ARG cc_start: 0.8663 (ptt-90) cc_final: 0.7869 (ptm160) REVERT: B 478 ARG cc_start: 0.8460 (mtm-85) cc_final: 0.8048 (mtm-85) REVERT: B 489 GLN cc_start: 0.7190 (OUTLIER) cc_final: 0.6930 (mm-40) outliers start: 15 outliers final: 7 residues processed: 119 average time/residue: 0.8070 time to fit residues: 100.6932 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 : 0.334 ------------------------------------------------------------------------------- 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 415 LEU 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 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: 1.9990 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 = 0.3343 r_free = 0.3343 target = 0.125794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.088985 restraints weight = 10880.718| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 1.50 r_work: 0.2717 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7804 Z= 0.204 Angle : 0.681 5.679 10594 Z= 0.348 Chirality : 0.045 0.154 1254 Planarity : 0.005 0.051 1222 Dihedral : 14.398 117.452 1656 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.54 % Allowed : 13.10 % 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 aren not related in a simple way. whole: 1.99 (0.27), residues: 910 helix: 2.02 (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 0.004 0.000 ARG A 32 TYR 0.022 0.003 TYR B 73 PHE 0.012 0.002 PHE B 240 TRP 0.009 0.002 TRP A 498 HIS 0.004 0.002 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 7802) covalent geometry : angle 0.67891 (10590) SS BOND : bond 0.00784 ( 2) SS BOND : angle 2.86503 ( 4) hydrogen bonds : bond 0.05970 ( 501) hydrogen bonds : angle 4.14308 ( 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 129 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.327 Fit side-chains REVERT: A 49 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8378 (tt) REVERT: A 179 LYS cc_start: 0.5996 (OUTLIER) cc_final: 0.5620 (pmtt) REVERT: A 292 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7793 (mppt) REVERT: A 415 LEU cc_start: 0.6948 (OUTLIER) cc_final: 0.6625 (tm) REVERT: A 442 ARG cc_start: 0.8721 (ptt-90) cc_final: 0.7965 (ptm160) REVERT: A 478 ARG cc_start: 0.8490 (mtm-85) cc_final: 0.8049 (mtm-85) REVERT: A 489 GLN cc_start: 0.7328 (OUTLIER) cc_final: 0.7057 (mm-40) REVERT: B 49 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8378 (tt) REVERT: B 179 LYS cc_start: 0.5999 (OUTLIER) cc_final: 0.5628 (pmtt) REVERT: B 292 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7788 (mppt) REVERT: B 415 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6620 (tm) REVERT: B 442 ARG cc_start: 0.8726 (ptt-90) cc_final: 0.7962 (ptm160) REVERT: B 478 ARG cc_start: 0.8483 (mtm-85) cc_final: 0.8040 (mtm-85) REVERT: B 489 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.7059 (mm-40) outliers start: 18 outliers final: 8 residues processed: 117 average time/residue: 0.7784 time to fit residues: 95.3185 Evaluate side-chains 129 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 292 LYS Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 415 LEU 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 292 LYS Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 415 LEU 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: 0.2980 chunk 21 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 0.0060 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 87 optimal weight: 0.2980 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3383 r_free = 0.3383 target = 0.128902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.094493 restraints weight = 6780.538| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 1.21 r_work: 0.2803 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7804 Z= 0.121 Angle : 0.544 5.021 10594 Z= 0.283 Chirality : 0.038 0.128 1254 Planarity : 0.004 0.042 1222 Dihedral : 13.620 115.412 1656 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.16 % Allowed : 13.61 % Favored : 84.22 % 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 aren not related in a simple way. whole: 2.44 (0.27), residues: 910 helix: 2.41 (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 0.002 0.000 ARG A 32 TYR 0.016 0.002 TYR A 73 PHE 0.012 0.001 PHE A 196 TRP 0.009 0.001 TRP B 186 HIS 0.002 0.001 HIS B 200 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 7802) covalent geometry : angle 0.54183 (10590) SS BOND : bond 0.00951 ( 2) SS BOND : angle 2.53857 ( 4) hydrogen bonds : bond 0.04447 ( 501) hydrogen bonds : angle 3.93601 ( 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: 15 poor density : 112 time to evaluate : 0.335 Fit side-chains REVERT: A 49 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8252 (tt) REVERT: A 61 PHE cc_start: 0.7749 (m-10) cc_final: 0.7105 (t80) REVERT: A 179 LYS cc_start: 0.5947 (OUTLIER) cc_final: 0.5607 (pmtt) REVERT: A 415 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6590 (tm) REVERT: A 442 ARG cc_start: 0.8609 (ptt-90) cc_final: 0.7818 (ptm160) REVERT: A 478 ARG cc_start: 0.8390 (mtm-85) cc_final: 0.7993 (mtp180) REVERT: A 489 GLN cc_start: 0.7144 (OUTLIER) cc_final: 0.6893 (mm-40) REVERT: B 49 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8251 (tt) REVERT: B 61 PHE cc_start: 0.7749 (m-10) cc_final: 0.7104 (t80) REVERT: B 179 LYS cc_start: 0.5946 (OUTLIER) cc_final: 0.5609 (pmtt) REVERT: B 442 ARG cc_start: 0.8613 (ptt-90) cc_final: 0.7815 (ptm160) REVERT: B 478 ARG cc_start: 0.8386 (mtm-85) cc_final: 0.7990 (mtp180) REVERT: B 489 GLN cc_start: 0.7145 (OUTLIER) cc_final: 0.6891 (mm-40) outliers start: 15 outliers final: 8 residues processed: 117 average time/residue: 0.7993 time to fit residues: 97.9831 Evaluate side-chains 127 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 415 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 84 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3367 r_free = 0.3367 target = 0.127647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.093177 restraints weight = 6690.735| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.19 r_work: 0.2780 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2655 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2655 r_free = 0.2655 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 = 0.2655 r_free = 0.2655 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1395 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= 0.144 Angle : 0.587 5.520 10594 Z= 0.303 Chirality : 0.040 0.137 1254 Planarity : 0.004 0.042 1222 Dihedral : 13.613 115.222 1656 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.16 % Allowed : 13.74 % Favored : 84.10 % 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 aren not related in a simple way. whole: 2.34 (0.27), residues: 910 helix: 2.33 (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 0.003 0.000 ARG A 32 TYR 0.019 0.002 TYR B 73 PHE 0.012 0.002 PHE A 196 TRP 0.007 0.001 TRP B 186 HIS 0.003 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 7802) covalent geometry : angle 0.58436 (10590) SS BOND : bond 0.00922 ( 2) SS BOND : angle 2.69446 ( 4) hydrogen bonds : bond 0.04996 ( 501) hydrogen bonds : angle 4.00172 ( 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 129 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.289 Fit side-chains REVERT: A 49 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8287 (tt) REVERT: A 61 PHE cc_start: 0.7784 (m-10) cc_final: 0.7123 (t80) REVERT: A 179 LYS cc_start: 0.5975 (OUTLIER) cc_final: 0.5623 (pmtt) REVERT: A 415 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6610 (tm) REVERT: A 442 ARG cc_start: 0.8622 (ptt-90) cc_final: 0.7844 (ptm160) REVERT: A 478 ARG cc_start: 0.8392 (mtm-85) cc_final: 0.7967 (mtm-85) REVERT: A 489 GLN cc_start: 0.7170 (OUTLIER) cc_final: 0.6867 (mm-40) REVERT: B 49 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8284 (tt) REVERT: B 61 PHE cc_start: 0.7779 (m-10) cc_final: 0.7121 (t80) REVERT: B 179 LYS cc_start: 0.5980 (OUTLIER) cc_final: 0.5631 (pmtt) REVERT: B 442 ARG cc_start: 0.8624 (ptt-90) cc_final: 0.7840 (ptm160) REVERT: B 478 ARG cc_start: 0.8389 (mtm-85) cc_final: 0.7965 (mtm-85) REVERT: B 489 GLN cc_start: 0.7167 (OUTLIER) cc_final: 0.6865 (mm-40) outliers start: 15 outliers final: 6 residues processed: 119 average time/residue: 0.7945 time to fit residues: 98.9777 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 : 0.313 ------------------------------------------------------------------------------- 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 415 LEU 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 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: 40.0000 chunk 30 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3357 r_free = 0.3357 target = 0.126958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.092276 restraints weight = 7411.182| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 1.22 r_work: 0.2756 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7804 Z= 0.166 Angle : 0.623 5.642 10594 Z= 0.320 Chirality : 0.042 0.141 1254 Planarity : 0.004 0.042 1222 Dihedral : 13.748 115.942 1656 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.04 % Allowed : 13.87 % Favored : 84.10 % 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 aren not related in a simple way. whole: 2.21 (0.27), residues: 910 helix: 2.20 (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 0.021 0.002 TYR B 73 PHE 0.012 0.002 PHE A 196 TRP 0.007 0.002 TRP A 498 HIS 0.003 0.001 HIS B 200 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 7802) covalent geometry : angle 0.62041 (10590) SS BOND : bond 0.00865 ( 2) SS BOND : angle 2.82388 ( 4) hydrogen bonds : bond 0.05398 ( 501) hydrogen bonds : angle 4.05488 ( 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 : 0.267 Fit side-chains REVERT: A 49 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8338 (tt) REVERT: A 61 PHE cc_start: 0.7800 (m-10) cc_final: 0.7159 (t80) REVERT: A 179 LYS cc_start: 0.5991 (OUTLIER) cc_final: 0.5638 (pmtt) REVERT: A 415 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6648 (tm) REVERT: A 442 ARG cc_start: 0.8661 (ptt-90) cc_final: 0.7907 (ptm160) REVERT: A 478 ARG cc_start: 0.8423 (mtm-85) cc_final: 0.7994 (mtm-85) REVERT: A 489 GLN cc_start: 0.7253 (OUTLIER) cc_final: 0.6947 (mm-40) REVERT: B 49 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8335 (tt) REVERT: B 61 PHE cc_start: 0.7793 (m-10) cc_final: 0.7152 (t80) REVERT: B 179 LYS cc_start: 0.5996 (OUTLIER) cc_final: 0.5646 (pmtt) REVERT: B 415 LEU cc_start: 0.6930 (OUTLIER) cc_final: 0.6642 (tm) REVERT: B 442 ARG cc_start: 0.8665 (ptt-90) cc_final: 0.7901 (ptm160) REVERT: B 478 ARG cc_start: 0.8427 (mtm-85) cc_final: 0.7997 (mtm-85) REVERT: B 489 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.6956 (mm-40) outliers start: 14 outliers final: 6 residues processed: 120 average time/residue: 0.7966 time to fit residues: 99.8934 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 : 0.308 ------------------------------------------------------------------------------- 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 415 LEU 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 305 GLU Chi-restraints excluded: chain B residue 415 LEU 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: 0.0010 chunk 19 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3391 r_free = 0.3391 target = 0.129573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.093605 restraints weight = 9222.887| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.41 r_work: 0.2774 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 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 = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7804 Z= 0.113 Angle : 0.529 4.976 10594 Z= 0.275 Chirality : 0.038 0.123 1254 Planarity : 0.004 0.041 1222 Dihedral : 13.236 114.942 1656 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.04 % Allowed : 13.87 % Favored : 84.10 % 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 aren not related in a simple way. whole: 2.56 (0.27), residues: 910 helix: 2.52 (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 A 32 TYR 0.016 0.002 TYR B 195 PHE 0.012 0.001 PHE A 196 TRP 0.009 0.001 TRP A 186 HIS 0.002 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 7802) covalent geometry : angle 0.52644 (10590) SS BOND : bond 0.00990 ( 2) SS BOND : angle 2.54167 ( 4) hydrogen bonds : bond 0.04253 ( 501) hydrogen bonds : angle 3.90071 ( 1437) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4493.93 seconds wall clock time: 77 minutes 17.33 seconds (4637.33 seconds total)