Starting phenix.real_space_refine on Wed Jan 15 01:10:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k69_36919/01_2025/8k69_36919.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k69_36919/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8k69_36919/01_2025/8k69_36919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k69_36919/01_2025/8k69_36919.map" model { file = "/net/cci-nas-00/data/ceres_data/8k69_36919/01_2025/8k69_36919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k69_36919/01_2025/8k69_36919.cif" } resolution = 2.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: {'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP: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: {'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP: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: {'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP: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: {'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP: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: 10.21, per 1000 atoms: 1.32 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: 2.16 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 0.72 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: 2.34 Time building geometry restraints manager: 2.41 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: 0.04 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: 7.730 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: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 27.150 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.260 ------------------------------------------------------------------------------- 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 7802 Z= 0.481 Angle : 0.939 9.520 10590 Z= 0.576 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (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 TRP 0.010 0.002 TRP B 527 HIS 0.004 0.002 HIS B 483 PHE 0.011 0.002 PHE A 196 TYR 0.019 0.002 TYR B 195 ARG 0.004 0.001 ARG B 32 *********************** 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 : 0.836 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: 1.4206 time to fit residues: 227.3126 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 : 0.780 ------------------------------------------------------------------------------- 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 75 optimal weight: 2.9990 chunk 68 optimal weight: 0.0970 chunk 37 optimal weight: 0.5980 chunk 23 optimal weight: 0.0270 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 42 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 overall best weight: 0.3636 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.131762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.097445 restraints weight = 8152.018| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.23 r_work: 0.2824 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 7802 Z= 0.132 Angle : 0.514 4.831 10590 Z= 0.268 Chirality : 0.037 0.126 1254 Planarity : 0.004 0.040 1222 Dihedral : 15.149 121.186 1704 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.67 % Allowed : 12.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.27), residues: 910 helix: 2.14 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.53 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 186 HIS 0.002 0.001 HIS A 37 PHE 0.008 0.001 PHE B 196 TYR 0.015 0.002 TYR A 195 ARG 0.002 0.000 ARG A 32 *********************** 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 146 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.817 Fit side-chains REVERT: A 414 LYS cc_start: 0.6365 (OUTLIER) cc_final: 0.5341 (tmtm) REVERT: A 415 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6526 (tm) REVERT: A 442 ARG cc_start: 0.8659 (ptt-90) cc_final: 0.7959 (ptm160) REVERT: A 478 ARG cc_start: 0.8471 (mtm-85) cc_final: 0.8047 (mtm-85) REVERT: A 480 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.7934 (mt0) REVERT: B 414 LYS cc_start: 0.6373 (OUTLIER) cc_final: 0.5353 (tmtm) REVERT: B 415 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6532 (tm) REVERT: B 442 ARG cc_start: 0.8667 (ptt-90) cc_final: 0.7962 (ptm160) REVERT: B 478 ARG cc_start: 0.8469 (mtm-85) cc_final: 0.8046 (mtm-85) REVERT: B 480 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7953 (mt0) outliers start: 21 outliers final: 6 residues processed: 138 average time/residue: 1.4831 time to fit residues: 214.7421 Evaluate side-chains 133 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 367 SER 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 367 SER 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 44 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 54 optimal weight: 0.0040 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 HIS B 483 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.129746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.095180 restraints weight = 8260.431| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.24 r_work: 0.2797 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2671 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2671 r_free = 0.2671 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2671 r_free = 0.2671 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2671 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7802 Z= 0.146 Angle : 0.525 4.944 10590 Z= 0.274 Chirality : 0.038 0.124 1254 Planarity : 0.004 0.039 1222 Dihedral : 13.692 113.235 1676 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.16 % Allowed : 12.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.27), residues: 910 helix: 2.43 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.53 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 186 HIS 0.002 0.001 HIS B 483 PHE 0.012 0.001 PHE B 196 TYR 0.016 0.002 TYR A 73 ARG 0.002 0.000 ARG A 32 *********************** 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 134 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.848 Fit side-chains REVERT: A 49 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8277 (tt) REVERT: A 61 PHE cc_start: 0.7771 (m-10) cc_final: 0.7257 (t80) REVERT: A 179 LYS cc_start: 0.5892 (OUTLIER) cc_final: 0.5099 (mmpt) REVERT: A 414 LYS cc_start: 0.6490 (OUTLIER) cc_final: 0.5467 (tmtm) REVERT: A 442 ARG cc_start: 0.8701 (ptt-90) cc_final: 0.7996 (ptm160) REVERT: A 478 ARG cc_start: 0.8521 (mtm-85) cc_final: 0.8192 (mtp180) REVERT: B 49 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8289 (tt) REVERT: B 61 PHE cc_start: 0.7769 (m-10) cc_final: 0.7255 (t80) REVERT: B 179 LYS cc_start: 0.5890 (OUTLIER) cc_final: 0.5154 (mmpt) REVERT: B 414 LYS cc_start: 0.6506 (OUTLIER) cc_final: 0.5483 (tmtm) REVERT: B 442 ARG cc_start: 0.8695 (ptt-90) cc_final: 0.7991 (ptm160) REVERT: B 478 ARG cc_start: 0.8523 (mtm-85) cc_final: 0.8196 (mtp180) outliers start: 17 outliers final: 5 residues processed: 128 average time/residue: 1.5773 time to fit residues: 211.6258 Evaluate side-chains 126 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 TYR 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 414 LYS 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 414 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 85 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3377 r_free = 0.3377 target = 0.128787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.092730 restraints weight = 12272.392| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 1.44 r_work: 0.2740 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7802 Z= 0.159 Angle : 0.541 5.106 10590 Z= 0.281 Chirality : 0.038 0.126 1254 Planarity : 0.004 0.038 1222 Dihedral : 13.013 112.549 1660 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.91 % Allowed : 13.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.27), residues: 910 helix: 2.46 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.47 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 186 HIS 0.002 0.001 HIS B 200 PHE 0.012 0.001 PHE A 196 TYR 0.017 0.002 TYR B 73 ARG 0.002 0.000 ARG A 32 *********************** 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 130 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.821 Fit side-chains REVERT: A 49 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8336 (tt) REVERT: A 61 PHE cc_start: 0.7898 (m-10) cc_final: 0.7275 (t80) REVERT: A 179 LYS cc_start: 0.5892 (OUTLIER) cc_final: 0.5585 (pmtt) REVERT: A 414 LYS cc_start: 0.6601 (OUTLIER) cc_final: 0.5564 (tmtm) REVERT: A 442 ARG cc_start: 0.8759 (ptt-90) cc_final: 0.8005 (ptm160) REVERT: A 478 ARG cc_start: 0.8590 (mtm-85) cc_final: 0.8245 (mtp180) REVERT: B 49 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8340 (tt) REVERT: B 61 PHE cc_start: 0.7901 (m-10) cc_final: 0.7284 (t80) REVERT: B 179 LYS cc_start: 0.5892 (OUTLIER) cc_final: 0.5588 (pmtt) REVERT: B 414 LYS cc_start: 0.6627 (OUTLIER) cc_final: 0.5588 (tmtm) REVERT: B 442 ARG cc_start: 0.8759 (ptt-90) cc_final: 0.8001 (ptm160) REVERT: B 478 ARG cc_start: 0.8586 (mtm-85) cc_final: 0.8240 (mtp180) outliers start: 15 outliers final: 5 residues processed: 122 average time/residue: 1.6225 time to fit residues: 207.6017 Evaluate side-chains 126 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 414 LYS 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 414 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3378 r_free = 0.3378 target = 0.128383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.093976 restraints weight = 11087.097| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 1.35 r_work: 0.2746 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2622 r_free = 0.2622 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2622 r_free = 0.2622 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7802 Z= 0.179 Angle : 0.559 5.186 10590 Z= 0.291 Chirality : 0.039 0.130 1254 Planarity : 0.004 0.038 1222 Dihedral : 12.938 114.041 1660 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.78 % Allowed : 13.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.27), residues: 910 helix: 2.42 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.48 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 498 HIS 0.003 0.001 HIS A 200 PHE 0.012 0.001 PHE A 196 TYR 0.018 0.002 TYR A 73 ARG 0.003 0.000 ARG A 32 *********************** 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 127 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 1.188 Fit side-chains REVERT: A 49 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8297 (tt) REVERT: A 61 PHE cc_start: 0.7789 (m-10) cc_final: 0.7581 (m-10) REVERT: A 179 LYS cc_start: 0.5905 (OUTLIER) cc_final: 0.5596 (pmtt) REVERT: A 442 ARG cc_start: 0.8681 (ptt-90) cc_final: 0.7887 (ptm160) REVERT: A 478 ARG cc_start: 0.8444 (mtm-85) cc_final: 0.8034 (mtp180) REVERT: B 49 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8295 (tt) REVERT: B 61 PHE cc_start: 0.7784 (m-10) cc_final: 0.7576 (m-10) REVERT: B 179 LYS cc_start: 0.5905 (OUTLIER) cc_final: 0.5600 (pmtt) REVERT: B 442 ARG cc_start: 0.8681 (ptt-90) cc_final: 0.7883 (ptm160) REVERT: B 478 ARG cc_start: 0.8441 (mtm-85) cc_final: 0.8031 (mtp180) outliers start: 12 outliers final: 6 residues processed: 119 average time/residue: 1.6834 time to fit residues: 210.2343 Evaluate side-chains 125 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 1.098 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 74 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 33 optimal weight: 50.0000 chunk 18 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 GLN B 480 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.126895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.091873 restraints weight = 7293.287| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 1.24 r_work: 0.2763 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- 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 = 0.41 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 | |-----------------------------------------------------------------------------| r_final: 0.2634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7802 Z= 0.227 Angle : 0.611 5.238 10590 Z= 0.315 Chirality : 0.041 0.136 1254 Planarity : 0.004 0.041 1222 Dihedral : 13.282 115.815 1652 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.16 % Allowed : 12.85 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.27), residues: 910 helix: 2.27 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.49 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 498 HIS 0.004 0.001 HIS A 200 PHE 0.012 0.002 PHE B 196 TYR 0.021 0.002 TYR B 73 ARG 0.003 0.000 ARG B 32 *********************** 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: 15 poor density : 115 time to evaluate : 0.913 Fit side-chains REVERT: A 49 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8323 (tt) REVERT: A 179 LYS cc_start: 0.5942 (OUTLIER) cc_final: 0.5599 (pmtt) REVERT: A 442 ARG cc_start: 0.8646 (ptt-90) cc_final: 0.7861 (ptm160) REVERT: A 478 ARG cc_start: 0.8390 (mtm-85) cc_final: 0.7941 (mtm-85) REVERT: B 49 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8323 (tt) REVERT: B 179 LYS cc_start: 0.5947 (OUTLIER) cc_final: 0.5605 (pmtt) REVERT: B 415 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6585 (tm) REVERT: B 442 ARG cc_start: 0.8648 (ptt-90) cc_final: 0.7857 (ptm160) REVERT: B 478 ARG cc_start: 0.8388 (mtm-85) cc_final: 0.7937 (mtm-85) outliers start: 15 outliers final: 6 residues processed: 120 average time/residue: 1.5976 time to fit residues: 201.2157 Evaluate side-chains 126 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 76 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 50.0000 chunk 59 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 GLN B 480 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.128757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.092136 restraints weight = 10251.780| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 1.52 r_work: 0.2750 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2631 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2631 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7802 Z= 0.163 Angle : 0.540 4.967 10590 Z= 0.282 Chirality : 0.038 0.126 1254 Planarity : 0.004 0.039 1222 Dihedral : 12.819 114.388 1652 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.91 % Allowed : 13.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.27), residues: 910 helix: 2.46 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.47 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 186 HIS 0.003 0.001 HIS B 200 PHE 0.012 0.001 PHE B 196 TYR 0.017 0.002 TYR B 73 ARG 0.002 0.000 ARG A 32 *********************** 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 128 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.946 Fit side-chains REVERT: A 49 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8270 (tt) REVERT: A 61 PHE cc_start: 0.7720 (m-10) cc_final: 0.7069 (t80) REVERT: A 179 LYS cc_start: 0.5887 (OUTLIER) cc_final: 0.5535 (pmtt) REVERT: A 442 ARG cc_start: 0.8668 (ptt-90) cc_final: 0.7845 (ptm160) REVERT: A 478 ARG cc_start: 0.8439 (mtm-85) cc_final: 0.8030 (mtp180) REVERT: B 49 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8271 (tt) REVERT: B 61 PHE cc_start: 0.7719 (m-10) cc_final: 0.7069 (t80) REVERT: B 179 LYS cc_start: 0.5894 (OUTLIER) cc_final: 0.5545 (pmtt) REVERT: B 442 ARG cc_start: 0.8668 (ptt-90) cc_final: 0.7842 (ptm160) REVERT: B 478 ARG cc_start: 0.8434 (mtm-85) cc_final: 0.8025 (mtp180) outliers start: 13 outliers final: 6 residues processed: 119 average time/residue: 1.6320 time to fit residues: 203.5740 Evaluate side-chains 125 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 47 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 0.1980 chunk 29 optimal weight: 0.0970 chunk 41 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3368 r_free = 0.3368 target = 0.127745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.092758 restraints weight = 7330.063| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 1.26 r_work: 0.2775 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- 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 = 0.43 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 = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7802 Z= 0.191 Angle : 0.574 5.028 10590 Z= 0.297 Chirality : 0.040 0.131 1254 Planarity : 0.004 0.039 1222 Dihedral : 12.992 114.555 1652 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.91 % Allowed : 13.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.27), residues: 910 helix: 2.37 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.50 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 498 HIS 0.003 0.001 HIS A 200 PHE 0.012 0.002 PHE B 196 TYR 0.019 0.002 TYR B 73 ARG 0.003 0.000 ARG A 32 *********************** 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 128 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.738 Fit side-chains REVERT: A 49 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8285 (tt) REVERT: A 61 PHE cc_start: 0.7700 (m-10) cc_final: 0.7074 (t80) REVERT: A 179 LYS cc_start: 0.5947 (OUTLIER) cc_final: 0.5604 (pmtt) REVERT: A 442 ARG cc_start: 0.8623 (ptt-90) cc_final: 0.7835 (ptm160) REVERT: A 478 ARG cc_start: 0.8379 (mtm-85) cc_final: 0.7968 (mtp180) REVERT: B 49 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8285 (tt) REVERT: B 61 PHE cc_start: 0.7695 (m-10) cc_final: 0.7076 (t80) REVERT: B 179 LYS cc_start: 0.5951 (OUTLIER) cc_final: 0.5608 (pmtt) REVERT: B 415 LEU cc_start: 0.6909 (OUTLIER) cc_final: 0.6614 (tm) REVERT: B 442 ARG cc_start: 0.8623 (ptt-90) cc_final: 0.7833 (ptm160) REVERT: B 478 ARG cc_start: 0.8374 (mtm-85) cc_final: 0.7962 (mtp180) outliers start: 13 outliers final: 6 residues processed: 120 average time/residue: 1.5528 time to fit residues: 195.1385 Evaluate side-chains 126 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 83 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 42 optimal weight: 0.1980 chunk 3 optimal weight: 4.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 = 0.3360 r_free = 0.3360 target = 0.127146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.091663 restraints weight = 8025.886| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 1.31 r_work: 0.2759 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- 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 = 0.43 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 = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7802 Z= 0.217 Angle : 0.603 5.136 10590 Z= 0.311 Chirality : 0.041 0.135 1254 Planarity : 0.004 0.039 1222 Dihedral : 13.254 115.940 1652 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.91 % Allowed : 13.10 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.27), residues: 910 helix: 2.27 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.48 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 498 HIS 0.003 0.001 HIS A 200 PHE 0.012 0.002 PHE B 196 TYR 0.020 0.002 TYR B 73 ARG 0.003 0.000 ARG B 32 *********************** 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 128 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.858 Fit side-chains REVERT: A 49 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8323 (tt) REVERT: A 61 PHE cc_start: 0.7742 (m-10) cc_final: 0.7104 (t80) REVERT: A 179 LYS cc_start: 0.5935 (OUTLIER) cc_final: 0.5584 (pmtt) REVERT: A 415 LEU cc_start: 0.6882 (OUTLIER) cc_final: 0.6586 (tm) REVERT: A 442 ARG cc_start: 0.8649 (ptt-90) cc_final: 0.7852 (ptm160) REVERT: A 478 ARG cc_start: 0.8416 (mtm-85) cc_final: 0.7996 (mtp180) REVERT: B 49 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8323 (tt) REVERT: B 61 PHE cc_start: 0.7742 (m-10) cc_final: 0.7106 (t80) REVERT: B 179 LYS cc_start: 0.5938 (OUTLIER) cc_final: 0.5588 (pmtt) REVERT: B 415 LEU cc_start: 0.6882 (OUTLIER) cc_final: 0.6588 (tm) REVERT: B 442 ARG cc_start: 0.8647 (ptt-90) cc_final: 0.7849 (ptm160) REVERT: B 478 ARG cc_start: 0.8409 (mtm-85) cc_final: 0.7989 (mtp180) outliers start: 13 outliers final: 6 residues processed: 121 average time/residue: 1.5564 time to fit residues: 197.4916 Evaluate side-chains 127 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 50 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 67 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3381 r_free = 0.3381 target = 0.128866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.093419 restraints weight = 8004.341| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 1.34 r_work: 0.2790 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 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 = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7802 Z= 0.160 Angle : 0.540 4.970 10590 Z= 0.281 Chirality : 0.038 0.125 1254 Planarity : 0.004 0.038 1222 Dihedral : 12.914 114.903 1652 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.78 % Allowed : 13.23 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.27), residues: 910 helix: 2.47 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.49 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 186 HIS 0.003 0.001 HIS B 200 PHE 0.012 0.001 PHE B 196 TYR 0.016 0.002 TYR A 195 ARG 0.002 0.000 ARG A 32 ********************** 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 125 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.869 Fit side-chains REVERT: A 49 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8270 (tt) REVERT: A 61 PHE cc_start: 0.7701 (m-10) cc_final: 0.7071 (t80) REVERT: A 179 LYS cc_start: 0.5925 (OUTLIER) cc_final: 0.5583 (pmtt) REVERT: A 415 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6600 (tm) REVERT: A 442 ARG cc_start: 0.8628 (ptt-90) cc_final: 0.7839 (ptm160) REVERT: A 478 ARG cc_start: 0.8391 (mtm-85) cc_final: 0.7984 (mtp180) REVERT: B 49 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8274 (tt) REVERT: B 61 PHE cc_start: 0.7699 (m-10) cc_final: 0.7072 (t80) REVERT: B 179 LYS cc_start: 0.5930 (OUTLIER) cc_final: 0.5588 (pmtt) REVERT: B 415 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.6612 (tm) REVERT: B 442 ARG cc_start: 0.8626 (ptt-90) cc_final: 0.7837 (ptm160) REVERT: B 478 ARG cc_start: 0.8388 (mtm-85) cc_final: 0.7981 (mtp180) outliers start: 12 outliers final: 6 residues processed: 119 average time/residue: 1.6168 time to fit residues: 202.6290 Evaluate side-chains 125 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.212 > 50: distance: 42 - 48: 9.820 distance: 48 - 49: 9.802 distance: 48 - 54: 5.359 distance: 49 - 50: 5.795 distance: 49 - 52: 8.979 distance: 50 - 51: 8.012 distance: 50 - 55: 9.055 distance: 52 - 53: 8.464 distance: 53 - 54: 10.221 distance: 55 - 56: 29.145 distance: 56 - 57: 19.944 distance: 56 - 59: 22.382 distance: 57 - 58: 30.533 distance: 57 - 62: 24.736 distance: 59 - 60: 13.891 distance: 60 - 61: 42.774 distance: 62 - 63: 15.356 distance: 63 - 64: 27.081 distance: 63 - 66: 16.145 distance: 64 - 65: 35.661 distance: 64 - 68: 9.206 distance: 66 - 67: 30.381 distance: 69 - 70: 33.821 distance: 69 - 72: 26.199 distance: 70 - 71: 26.136 distance: 70 - 75: 23.172 distance: 72 - 73: 41.255 distance: 72 - 74: 43.420 distance: 75 - 76: 19.326 distance: 75 - 155: 32.381 distance: 76 - 77: 28.189 distance: 76 - 79: 27.602 distance: 77 - 78: 22.119 distance: 77 - 82: 12.582 distance: 78 - 152: 18.924 distance: 79 - 80: 15.369 distance: 79 - 81: 3.886 distance: 82 - 83: 26.789 distance: 83 - 84: 32.174 distance: 83 - 86: 22.769 distance: 84 - 85: 19.922 distance: 84 - 93: 24.078 distance: 86 - 87: 22.603 distance: 87 - 88: 20.329 distance: 87 - 89: 11.721 distance: 88 - 90: 29.769 distance: 89 - 91: 13.101 distance: 90 - 92: 9.212 distance: 91 - 92: 13.604 distance: 93 - 94: 17.461 distance: 94 - 95: 19.470 distance: 94 - 97: 22.700 distance: 95 - 96: 19.352 distance: 95 - 98: 32.873 distance: 99 - 100: 23.211 distance: 99 - 102: 51.929 distance: 100 - 101: 26.665 distance: 100 - 106: 17.080 distance: 102 - 103: 15.420 distance: 103 - 104: 16.619 distance: 103 - 105: 25.840 distance: 106 - 107: 32.133 distance: 107 - 108: 34.373 distance: 107 - 110: 16.285 distance: 108 - 109: 29.834 distance: 108 - 111: 7.126 distance: 111 - 112: 18.641 distance: 112 - 113: 41.068 distance: 112 - 115: 31.987 distance: 113 - 114: 19.685 distance: 113 - 116: 22.808