Starting phenix.real_space_refine on Thu Jul 2 08:01:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k69_36919/07_2026/8k69_36919.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k69_36919/07_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_36919/07_2026/8k69_36919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k69_36919/07_2026/8k69_36919.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k69_36919/07_2026/8k69_36919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k69_36919/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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, 229 Ad-hoc single atom residues: {' NA': 3} Unusual residues: {'CLR': 1, 'PC1': 1, 'PTY': 1, 'T7X': 1, 'Y01': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain breaks: 3 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, 229 Ad-hoc single atom residues: {' NA': 3} Unusual residues: {'CLR': 1, 'PC1': 1, 'PTY': 1, 'T7X': 1, 'Y01': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain breaks: 3 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: 2.33, 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: 0.66 Conformation dependent library (CDL) restraints added in 339.1 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: 0.17 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: 1.00 Time building geometry restraints manager: 0.80 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 3.210 nonbonded pdb="NA NA A 607 " pdb=" O HOH A 701 " model vdw 2.100 3.210 ... (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: 9.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.070 Find NCS groups from input model: 0.150 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:7.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.500 ------------------------------------------------------------------------------- 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 : 0.312 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: 0.6330 time to fit residues: 101.3747 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 : 0.239 ------------------------------------------------------------------------------- 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: 2.9990 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: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 200 HIS A 251 ASN A 421 ASN A 483 HIS B 39 HIS B 200 HIS B 251 ASN B 421 ASN B 483 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.128861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.093524 restraints weight = 9663.187| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.30 r_work: 0.2762 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7804 Z= 0.138 Angle : 0.578 5.033 10594 Z= 0.302 Chirality : 0.040 0.126 1254 Planarity : 0.004 0.043 1222 Dihedral : 14.580 104.610 1630 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.93 % Allowed : 11.96 % Favored : 85.11 % 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: 1.82 (0.27), residues: 910 helix: 1.88 (0.19), residues: 646 sheet: None (None), residues: 0 loop : -0.43 (0.35), 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 0.010 0.001 PHE B 196 TRP 0.008 0.001 TRP B 186 HIS 0.002 0.001 HIS A 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 ( 7802) covalent geometry : angle 0.57355 / 0.30 (10590) SS BOND : bond 0.00888 / 0.45 ( 2) SS BOND : angle 3.80307 / 2.31 ( 4) hydrogen bonds : bond 0.04957 / 3.35 ( 501) hydrogen bonds : angle 4.07639 / 3.04 ( 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: 23 poor density : 122 time to evaluate : 0.270 Fit side-chains REVERT: A 414 LYS cc_start: 0.6428 (OUTLIER) cc_final: 0.5439 (tmtm) REVERT: A 415 LEU cc_start: 0.6863 (OUTLIER) cc_final: 0.6562 (tm) REVERT: A 442 ARG cc_start: 0.8719 (ptt-90) cc_final: 0.7987 (ptm160) REVERT: A 478 ARG cc_start: 0.8493 (mtm-85) cc_final: 0.8055 (mtm-85) REVERT: A 480 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.8119 (mt0) REVERT: A 525 GLU cc_start: 0.8684 (tp30) cc_final: 0.8457 (tp30) REVERT: B 414 LYS cc_start: 0.6431 (OUTLIER) cc_final: 0.5442 (tmtm) REVERT: B 415 LEU cc_start: 0.6863 (OUTLIER) cc_final: 0.6567 (tm) REVERT: B 442 ARG cc_start: 0.8722 (ptt-90) cc_final: 0.7992 (ptm160) REVERT: B 478 ARG cc_start: 0.8493 (mtm-85) cc_final: 0.8057 (mtm-85) REVERT: B 480 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8123 (mt0) REVERT: B 525 GLU cc_start: 0.8682 (tp30) cc_final: 0.8454 (tp30) outliers start: 23 outliers final: 8 residues processed: 133 average time/residue: 0.6235 time to fit residues: 86.8935 Evaluate side-chains 130 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 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 49 LEU Chi-restraints excluded: chain B residue 54 LEU 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: 1.9990 chunk 48 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.128811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.093436 restraints weight = 9270.770| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.32 r_work: 0.2774 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- 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 = 0.37 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: 0.9052 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7804 Z= 0.128 Angle : 0.553 4.963 10594 Z= 0.289 Chirality : 0.039 0.128 1254 Planarity : 0.004 0.042 1222 Dihedral : 12.848 92.773 1600 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.05 % Allowed : 11.83 % Favored : 85.11 % 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: 2.30 (0.27), residues: 910 helix: 2.27 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.34 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 32 TYR 0.017 0.002 TYR A 73 PHE 0.012 0.001 PHE B 196 TRP 0.007 0.001 TRP A 186 HIS 0.002 0.001 HIS A 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 ( 7802) covalent geometry : angle 0.54971 / 0.29 (10590) SS BOND : bond 0.01066 / 0.53 ( 2) SS BOND : angle 3.12955 / 1.90 ( 4) hydrogen bonds : bond 0.04680 / 3.16 ( 501) hydrogen bonds : angle 3.97726 / 2.97 ( 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: 24 poor density : 113 time to evaluate : 0.290 Fit side-chains REVERT: A 179 LYS cc_start: 0.5904 (OUTLIER) cc_final: 0.5495 (pptt) REVERT: A 414 LYS cc_start: 0.6593 (OUTLIER) cc_final: 0.5606 (tmtm) REVERT: A 442 ARG cc_start: 0.8713 (ptt-90) cc_final: 0.7992 (ptm160) REVERT: A 478 ARG cc_start: 0.8544 (mtm-85) cc_final: 0.8197 (mtm-85) REVERT: A 489 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.7063 (mm-40) REVERT: B 179 LYS cc_start: 0.5913 (OUTLIER) cc_final: 0.5503 (pptt) REVERT: B 414 LYS cc_start: 0.6607 (OUTLIER) cc_final: 0.5623 (tmtm) REVERT: B 442 ARG cc_start: 0.8715 (ptt-90) cc_final: 0.7990 (ptm160) REVERT: B 478 ARG cc_start: 0.8544 (mtm-85) cc_final: 0.8200 (mtm-85) REVERT: B 489 GLN cc_start: 0.7302 (OUTLIER) cc_final: 0.7079 (mm-40) outliers start: 24 outliers final: 10 residues processed: 125 average time/residue: 0.6462 time to fit residues: 84.6927 Evaluate side-chains 129 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.204 ------------------------------------------------------------------------------- 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 300 ILE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 414 LYS 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 300 ILE Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 414 LYS Chi-restraints excluded: chain B residue 489 GLN 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: 0.5980 chunk 81 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 1 optimal weight: 0.0670 chunk 7 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- 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 = 0.3378 r_free = 0.3378 target = 0.128808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.093065 restraints weight = 8339.991| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 1.29 r_work: 0.2775 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.2650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.1350 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= 0.131 Angle : 0.561 5.098 10594 Z= 0.292 Chirality : 0.039 0.131 1254 Planarity : 0.004 0.041 1222 Dihedral : 12.378 84.647 1586 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.42 % Allowed : 12.98 % 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: 2.43 (0.27), residues: 910 helix: 2.37 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.33 (0.35), 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 B 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 0.00271 / 0.13 ( 7802) covalent geometry : angle 0.55804 / 0.29 (10590) SS BOND : bond 0.00891 / 0.45 ( 2) SS BOND : angle 2.87983 / 1.74 ( 4) hydrogen bonds : bond 0.04735 / 3.19 ( 501) hydrogen bonds : angle 3.98536 / 2.98 ( 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 133 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.335 Fit side-chains REVERT: A 61 PHE cc_start: 0.7696 (m-10) cc_final: 0.7099 (t80) REVERT: A 179 LYS cc_start: 0.5887 (OUTLIER) cc_final: 0.5579 (pmtt) REVERT: A 414 LYS cc_start: 0.6545 (OUTLIER) cc_final: 0.5508 (tmtm) REVERT: A 442 ARG cc_start: 0.8644 (ptt-90) cc_final: 0.7847 (ptm160) REVERT: A 478 ARG cc_start: 0.8417 (mtm-85) cc_final: 0.7992 (mtm-85) REVERT: A 489 GLN cc_start: 0.7171 (OUTLIER) cc_final: 0.6929 (mm-40) REVERT: B 61 PHE cc_start: 0.7691 (m-10) cc_final: 0.7092 (t80) REVERT: B 179 LYS cc_start: 0.5913 (OUTLIER) cc_final: 0.5606 (pmtt) REVERT: B 414 LYS cc_start: 0.6549 (OUTLIER) cc_final: 0.5509 (tmtm) REVERT: B 442 ARG cc_start: 0.8642 (ptt-90) cc_final: 0.7847 (ptm160) REVERT: B 478 ARG cc_start: 0.8419 (mtm-85) cc_final: 0.7997 (mtm-85) REVERT: B 489 GLN cc_start: 0.7175 (OUTLIER) cc_final: 0.6932 (mm-40) outliers start: 19 outliers final: 8 residues processed: 123 average time/residue: 0.6162 time to fit residues: 79.5368 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 : 0.259 ------------------------------------------------------------------------------- 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 399 LEU Chi-restraints excluded: chain A residue 414 LYS 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 399 LEU Chi-restraints excluded: chain B residue 414 LYS Chi-restraints excluded: chain B residue 489 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 52 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 47 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 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: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3365 r_free = 0.3365 target = 0.127506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.091872 restraints weight = 7895.620| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 1.32 r_work: 0.2759 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 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 = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7804 Z= 0.156 Angle : 0.608 5.559 10594 Z= 0.314 Chirality : 0.041 0.147 1254 Planarity : 0.004 0.041 1222 Dihedral : 12.526 83.593 1586 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.54 % Allowed : 12.72 % 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: 2.31 (0.27), residues: 910 helix: 2.27 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.32 (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 A 73 PHE 0.012 0.002 PHE B 196 TRP 0.007 0.001 TRP B 498 HIS 0.003 0.001 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 ( 7802) covalent geometry : angle 0.60603 / 0.31 (10590) SS BOND : bond 0.00833 / 0.42 ( 2) SS BOND : angle 2.86169 / 1.72 ( 4) hydrogen bonds : bond 0.05242 / 3.53 ( 501) hydrogen bonds : angle 4.04834 / 3.02 ( 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: 18 poor density : 114 time to evaluate : 0.216 Fit side-chains REVERT: A 61 PHE cc_start: 0.7773 (m-10) cc_final: 0.7154 (t80) REVERT: A 179 LYS cc_start: 0.5935 (OUTLIER) cc_final: 0.5524 (pptt) REVERT: A 442 ARG cc_start: 0.8643 (ptt-90) cc_final: 0.7850 (ptm160) REVERT: A 478 ARG cc_start: 0.8415 (mtm-85) cc_final: 0.7971 (mtm-85) REVERT: A 480 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8197 (mt0) REVERT: A 489 GLN cc_start: 0.7187 (OUTLIER) cc_final: 0.6929 (mm-40) REVERT: B 61 PHE cc_start: 0.7769 (m-10) cc_final: 0.7153 (t80) REVERT: B 179 LYS cc_start: 0.5940 (OUTLIER) cc_final: 0.5529 (pptt) REVERT: B 442 ARG cc_start: 0.8647 (ptt-90) cc_final: 0.7847 (ptm160) REVERT: B 478 ARG cc_start: 0.8415 (mtm-85) cc_final: 0.7976 (mtm-85) REVERT: B 480 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8200 (mt0) REVERT: B 489 GLN cc_start: 0.7183 (OUTLIER) cc_final: 0.6921 (mm-40) outliers start: 18 outliers final: 10 residues processed: 120 average time/residue: 0.6363 time to fit residues: 80.0482 Evaluate side-chains 130 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.209 ------------------------------------------------------------------------------- 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 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 300 ILE Chi-restraints excluded: chain B residue 305 GLU 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: 0.9980 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 33 optimal weight: 50.0000 chunk 1 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.128698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.092433 restraints weight = 9549.881| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 1.42 r_work: 0.2747 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 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 = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7804 Z= 0.133 Angle : 0.563 5.247 10594 Z= 0.293 Chirality : 0.039 0.131 1254 Planarity : 0.004 0.040 1222 Dihedral : 11.813 79.864 1578 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % 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: 2.48 (0.27), residues: 910 helix: 2.40 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.27 (0.35), 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 B 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 7802) covalent geometry : angle 0.56091 / 0.29 (10590) SS BOND : bond 0.00909 / 0.46 ( 2) SS BOND : angle 2.65746 / 1.60 ( 4) hydrogen bonds : bond 0.04731 / 3.19 ( 501) hydrogen bonds : angle 3.96774 / 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 130 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.207 Fit side-chains REVERT: A 61 PHE cc_start: 0.7805 (m-10) cc_final: 0.7177 (t80) REVERT: A 179 LYS cc_start: 0.5923 (OUTLIER) cc_final: 0.5560 (pmtt) REVERT: A 442 ARG cc_start: 0.8660 (ptt-90) cc_final: 0.7844 (ptm160) REVERT: A 478 ARG cc_start: 0.8445 (mtm-85) cc_final: 0.8014 (mtm-85) REVERT: A 489 GLN cc_start: 0.7185 (OUTLIER) cc_final: 0.6927 (mm-40) REVERT: B 61 PHE cc_start: 0.7806 (m-10) cc_final: 0.7173 (t80) REVERT: B 179 LYS cc_start: 0.5926 (OUTLIER) cc_final: 0.5567 (pmtt) REVERT: B 442 ARG cc_start: 0.8661 (ptt-90) cc_final: 0.7841 (ptm160) REVERT: B 478 ARG cc_start: 0.8444 (mtm-85) cc_final: 0.8015 (mtm-85) REVERT: B 489 GLN cc_start: 0.7189 (OUTLIER) cc_final: 0.6929 (mm-40) outliers start: 16 outliers final: 8 residues processed: 119 average time/residue: 0.6249 time to fit residues: 77.8847 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 : 0.285 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 16 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.3350 r_free = 0.3350 target = 0.126411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.089551 restraints weight = 10418.210| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 1.50 r_work: 0.2705 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.1279 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= 0.190 Angle : 0.661 5.967 10594 Z= 0.339 Chirality : 0.044 0.153 1254 Planarity : 0.005 0.049 1222 Dihedral : 12.350 82.598 1578 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.77 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: 2.15 (0.27), residues: 910 helix: 2.11 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.28 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 32 TYR 0.021 0.003 TYR B 73 PHE 0.012 0.002 PHE B 240 TRP 0.008 0.002 TRP A 498 HIS 0.004 0.002 HIS B 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.19 ( 7802) covalent geometry : angle 0.65879 / 0.34 (10590) SS BOND : bond 0.00810 / 0.41 ( 2) SS BOND : angle 2.90425 / 1.72 ( 4) hydrogen bonds : bond 0.05750 / 3.88 ( 501) hydrogen bonds : angle 4.11308 / 3.07 ( 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 131 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.209 Fit side-chains REVERT: A 179 LYS cc_start: 0.5937 (OUTLIER) cc_final: 0.5575 (pmtt) REVERT: A 292 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7749 (mppt) REVERT: A 442 ARG cc_start: 0.8703 (ptt-90) cc_final: 0.7883 (ptm160) REVERT: A 478 ARG cc_start: 0.8471 (mtm-85) cc_final: 0.8014 (mtm-85) REVERT: A 489 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.6976 (mm-40) REVERT: B 179 LYS cc_start: 0.5941 (OUTLIER) cc_final: 0.5579 (pmtt) REVERT: B 292 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7774 (mppt) REVERT: B 442 ARG cc_start: 0.8704 (ptt-90) cc_final: 0.7878 (ptm160) REVERT: B 478 ARG cc_start: 0.8462 (mtm-85) cc_final: 0.8004 (mtm-85) REVERT: B 489 GLN cc_start: 0.7270 (OUTLIER) cc_final: 0.6962 (mm-40) outliers start: 16 outliers final: 10 residues processed: 119 average time/residue: 0.6359 time to fit residues: 79.4963 Evaluate side-chains 130 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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 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 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: 0.8980 chunk 56 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 GLN 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 = 0.129097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.094629 restraints weight = 6750.314| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 1.20 r_work: 0.2789 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2677 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 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 = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7804 Z= 0.126 Angle : 0.549 4.969 10594 Z= 0.287 Chirality : 0.038 0.126 1254 Planarity : 0.004 0.040 1222 Dihedral : 11.701 79.484 1578 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.67 % Allowed : 13.10 % 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 are not related in a simple way. whole: 2.52 (0.27), residues: 910 helix: 2.42 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.24 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 32 TYR 0.017 0.002 TYR A 73 PHE 0.012 0.001 PHE A 196 TRP 0.007 0.001 TRP A 186 HIS 0.002 0.001 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 ( 7802) covalent geometry : angle 0.54681 / 0.29 (10590) SS BOND : bond 0.00911 / 0.46 ( 2) SS BOND : angle 2.58546 / 1.54 ( 4) hydrogen bonds : bond 0.04574 / 3.08 ( 501) hydrogen bonds : angle 3.95718 / 2.95 ( 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 130 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.303 Fit side-chains REVERT: A 61 PHE cc_start: 0.7688 (m-10) cc_final: 0.7081 (t80) REVERT: A 179 LYS cc_start: 0.5961 (OUTLIER) cc_final: 0.5615 (pmtt) REVERT: A 292 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7744 (mppt) REVERT: A 442 ARG cc_start: 0.8603 (ptt-90) cc_final: 0.7814 (ptm160) REVERT: A 478 ARG cc_start: 0.8378 (mtm-85) cc_final: 0.7974 (mtp180) REVERT: A 489 GLN cc_start: 0.7138 (OUTLIER) cc_final: 0.6876 (mm-40) REVERT: B 61 PHE cc_start: 0.7686 (m-10) cc_final: 0.7077 (t80) REVERT: B 179 LYS cc_start: 0.5967 (OUTLIER) cc_final: 0.5620 (pmtt) REVERT: B 292 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7729 (mppt) REVERT: B 442 ARG cc_start: 0.8601 (ptt-90) cc_final: 0.7808 (ptm160) REVERT: B 478 ARG cc_start: 0.8377 (mtm-85) cc_final: 0.7973 (mtp180) REVERT: B 489 GLN cc_start: 0.7136 (OUTLIER) cc_final: 0.6872 (mm-40) outliers start: 19 outliers final: 8 residues processed: 115 average time/residue: 0.6843 time to fit residues: 82.6705 Evaluate side-chains 125 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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 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 292 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: 1.9990 chunk 44 optimal weight: 0.8980 chunk 72 optimal weight: 0.0970 chunk 7 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.127232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.092745 restraints weight = 6645.393| |-----------------------------------------------------------------------------| r_work (start): 0.2880 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: 0.2645 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 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 = 0.2645 r_free = 0.2645 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: 0.2645 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7804 Z= 0.168 Angle : 0.626 5.285 10594 Z= 0.323 Chirality : 0.042 0.136 1254 Planarity : 0.004 0.042 1222 Dihedral : 12.125 81.392 1578 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.42 % Allowed : 13.49 % 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 are not related in a simple way. whole: 2.26 (0.27), residues: 910 helix: 2.21 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.28 (0.36), 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 B 196 TRP 0.007 0.002 TRP B 498 HIS 0.004 0.002 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 ( 7802) covalent geometry : angle 0.62355 / 0.32 (10590) SS BOND : bond 0.00850 / 0.43 ( 2) SS BOND : angle 2.81573 / 1.67 ( 4) hydrogen bonds : bond 0.05414 / 3.65 ( 501) hydrogen bonds : angle 4.06727 / 3.04 ( 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 131 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.199 Fit side-chains REVERT: A 61 PHE cc_start: 0.7748 (m-10) cc_final: 0.7116 (t80) REVERT: A 179 LYS cc_start: 0.5989 (OUTLIER) cc_final: 0.5638 (pmtt) REVERT: A 292 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7746 (mppt) REVERT: A 442 ARG cc_start: 0.8634 (ptt-90) cc_final: 0.7857 (ptm160) REVERT: A 478 ARG cc_start: 0.8394 (mtm-85) cc_final: 0.7947 (mtm-85) REVERT: A 489 GLN cc_start: 0.7187 (OUTLIER) cc_final: 0.6883 (mm-40) REVERT: B 61 PHE cc_start: 0.7749 (m-10) cc_final: 0.7115 (t80) REVERT: B 179 LYS cc_start: 0.5986 (OUTLIER) cc_final: 0.5641 (pmtt) REVERT: B 292 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7751 (mppt) REVERT: B 442 ARG cc_start: 0.8635 (ptt-90) cc_final: 0.7850 (ptm160) REVERT: B 478 ARG cc_start: 0.8389 (mtm-85) cc_final: 0.7943 (mtm-85) REVERT: B 489 GLN cc_start: 0.7185 (OUTLIER) cc_final: 0.6882 (mm-40) outliers start: 17 outliers final: 10 residues processed: 118 average time/residue: 0.7069 time to fit residues: 87.4853 Evaluate side-chains 130 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 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 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: 0.6980 chunk 13 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3372 r_free = 0.3372 target = 0.128186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.093232 restraints weight = 7351.432| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 1.24 r_work: 0.2771 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.1417 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= 0.142 Angle : 0.580 5.008 10594 Z= 0.301 Chirality : 0.040 0.130 1254 Planarity : 0.004 0.041 1222 Dihedral : 11.910 80.314 1578 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % 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 are not related in a simple way. whole: 2.39 (0.27), residues: 910 helix: 2.32 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.29 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 32 TYR 0.018 0.002 TYR A 73 PHE 0.012 0.002 PHE B 196 TRP 0.006 0.001 TRP B 498 HIS 0.003 0.001 HIS B 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 7802) covalent geometry : angle 0.57805 / 0.30 (10590) SS BOND : bond 0.00900 / 0.45 ( 2) SS BOND : angle 2.69671 / 1.60 ( 4) hydrogen bonds : bond 0.04925 / 3.32 ( 501) hydrogen bonds : angle 4.00473 / 2.99 ( 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 : 0.318 Fit side-chains REVERT: A 61 PHE cc_start: 0.7755 (m-10) cc_final: 0.7098 (t80) REVERT: A 179 LYS cc_start: 0.5958 (OUTLIER) cc_final: 0.5600 (pmtt) REVERT: A 292 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7744 (mppt) REVERT: A 442 ARG cc_start: 0.8630 (ptt-90) cc_final: 0.7847 (ptm160) REVERT: A 478 ARG cc_start: 0.8399 (mtm-85) cc_final: 0.7960 (mtm-85) REVERT: A 489 GLN cc_start: 0.7159 (OUTLIER) cc_final: 0.6907 (mm-40) REVERT: B 61 PHE cc_start: 0.7755 (m-10) cc_final: 0.7097 (t80) REVERT: B 179 LYS cc_start: 0.5962 (OUTLIER) cc_final: 0.5604 (pmtt) REVERT: B 292 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7774 (mppt) REVERT: B 442 ARG cc_start: 0.8631 (ptt-90) cc_final: 0.7844 (ptm160) REVERT: B 478 ARG cc_start: 0.8398 (mtm-85) cc_final: 0.7959 (mtm-85) REVERT: B 489 GLN cc_start: 0.7162 (OUTLIER) cc_final: 0.6909 (mm-40) outliers start: 14 outliers final: 8 residues processed: 118 average time/residue: 0.6835 time to fit residues: 84.9007 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 : 0.325 ------------------------------------------------------------------------------- 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 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 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: 0.8980 chunk 19 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.129226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.093078 restraints weight = 9013.011| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 1.39 r_work: 0.2775 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- 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 = 0.42 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: 3 (3 function evaluations) r_final: 0.2657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 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 : 0.003 0.026 7804 Z= 0.125 Angle : 0.548 4.980 10594 Z= 0.286 Chirality : 0.038 0.123 1254 Planarity : 0.004 0.040 1222 Dihedral : 11.646 79.169 1578 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.91 % Allowed : 13.87 % 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 are not related in a simple way. whole: 2.53 (0.27), residues: 910 helix: 2.44 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.28 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 32 TYR 0.017 0.002 TYR A 73 PHE 0.012 0.001 PHE B 196 TRP 0.007 0.001 TRP A 186 HIS 0.002 0.001 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 ( 7802) covalent geometry : angle 0.54537 / 0.29 (10590) SS BOND : bond 0.00927 / 0.47 ( 2) SS BOND : angle 2.60721 / 1.55 ( 4) hydrogen bonds : bond 0.04545 / 3.06 ( 501) hydrogen bonds : angle 3.94055 / 2.94 ( 1437) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3833.76 seconds wall clock time: 66 minutes 0.03 seconds (3960.03 seconds total)