Starting phenix.real_space_refine on Sat Aug 3 09:20:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k69_36919/08_2024/8k69_36919.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k69_36919/08_2024/8k69_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k69_36919/08_2024/8k69_36919.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k69_36919/08_2024/8k69_36919.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k69_36919/08_2024/8k69_36919.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k69_36919/08_2024/8k69_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 Residue "A GLU 68": "OE1" <-> "OE2" Residue "A GLU 114": "OE1" <-> "OE2" Residue "A ARG 125": "NH1" <-> "NH2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A ARG 281": "NH1" <-> "NH2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 460": "OE1" <-> "OE2" Residue "A ARG 478": "NH1" <-> "NH2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B GLU 114": "OE1" <-> "OE2" Residue "B ARG 125": "NH1" <-> "NH2" Residue "B ARG 213": "NH1" <-> "NH2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B ARG 281": "NH1" <-> "NH2" Residue "B ARG 365": "NH1" <-> "NH2" Residue "B PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 460": "OE1" <-> "OE2" Residue "B ARG 478": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 9.22, per 1000 atoms: 1.19 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 - 3.50 Amino acid : False - 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: 3.59 Conformation dependent library (CDL) restraints added in 2.3 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: 0.70 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: 2.03 Time building geometry restraints manager: 3.60 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: 100.24 - 107.03: 224 107.03 - 113.82: 4513 113.82 - 120.61: 3388 120.61 - 127.40: 2397 127.40 - 134.19: 68 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 487 or resid 489 through 530 or resid 602 or re \ sid 607 through 609)) selection = (chain 'B' and (resid 22 through 487 or resid 489 through 530 or resid 702 or re \ sid 707 through 709)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.920 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: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 30.010 Find NCS groups from input model: 0.300 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:11.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.380 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 44 poor density : 124 time to evaluate : 0.810 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: 1.3282 time to fit residues: 212.4818 Evaluate side-chains 145 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 121 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 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 fitting. rotamer outliers: 21 poor density : 125 time to evaluate : 0.855 Fit side-chains REVERT: A 414 LYS cc_start: 0.5739 (OUTLIER) cc_final: 0.4734 (tmtm) REVERT: A 415 LEU cc_start: 0.6322 (OUTLIER) cc_final: 0.5916 (tm) REVERT: A 442 ARG cc_start: 0.7085 (ptt-90) cc_final: 0.5857 (ptm160) REVERT: A 478 ARG cc_start: 0.7339 (mtm-85) cc_final: 0.6629 (mtm-85) REVERT: A 480 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.6865 (mt0) REVERT: A 489 GLN cc_start: 0.6199 (mm-40) cc_final: 0.5926 (mm-40) REVERT: B 414 LYS cc_start: 0.5741 (OUTLIER) cc_final: 0.4735 (tmtm) REVERT: B 415 LEU cc_start: 0.6319 (OUTLIER) cc_final: 0.5915 (tm) REVERT: B 442 ARG cc_start: 0.7086 (ptt-90) cc_final: 0.5862 (ptm160) REVERT: B 478 ARG cc_start: 0.7339 (mtm-85) cc_final: 0.6631 (mtm-85) REVERT: B 480 GLN cc_start: 0.7589 (OUTLIER) cc_final: 0.6881 (mt0) REVERT: B 489 GLN cc_start: 0.6213 (mm-40) cc_final: 0.5942 (mm-40) outliers start: 21 outliers final: 6 residues processed: 138 average time/residue: 1.3437 time to fit residues: 195.1111 Evaluate side-chains 133 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 121 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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 45 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7802 Z= 0.177 Angle : 0.566 5.030 10590 Z= 0.294 Chirality : 0.039 0.130 1254 Planarity : 0.004 0.041 1222 Dihedral : 14.270 115.835 1676 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.67 % Allowed : 12.21 % 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: 2.25 (0.27), residues: 910 helix: 2.28 (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 B 483 PHE 0.012 0.001 PHE B 196 TYR 0.018 0.002 TYR B 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 140 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 0.857 Fit side-chains REVERT: A 49 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7103 (tt) REVERT: A 61 PHE cc_start: 0.6701 (m-10) cc_final: 0.5930 (t80) REVERT: A 179 LYS cc_start: 0.5585 (OUTLIER) cc_final: 0.4842 (mmpt) REVERT: A 414 LYS cc_start: 0.5952 (OUTLIER) cc_final: 0.4919 (tmtm) REVERT: A 415 LEU cc_start: 0.6389 (OUTLIER) cc_final: 0.5898 (tm) REVERT: A 442 ARG cc_start: 0.7130 (ptt-90) cc_final: 0.5904 (ptm160) REVERT: A 478 ARG cc_start: 0.7371 (mtm-85) cc_final: 0.6774 (mtp180) REVERT: A 489 GLN cc_start: 0.6249 (mm-40) cc_final: 0.5945 (mm-40) REVERT: B 49 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7114 (tt) REVERT: B 61 PHE cc_start: 0.6688 (m-10) cc_final: 0.5912 (t80) REVERT: B 179 LYS cc_start: 0.5582 (OUTLIER) cc_final: 0.4840 (mmpt) REVERT: B 414 LYS cc_start: 0.5955 (OUTLIER) cc_final: 0.4922 (tmtm) REVERT: B 415 LEU cc_start: 0.6391 (OUTLIER) cc_final: 0.5897 (tm) REVERT: B 442 ARG cc_start: 0.7130 (ptt-90) cc_final: 0.5904 (ptm160) REVERT: B 478 ARG cc_start: 0.7369 (mtm-85) cc_final: 0.6771 (mtp180) REVERT: B 489 GLN cc_start: 0.6272 (mm-40) cc_final: 0.5978 (mm-40) outliers start: 21 outliers final: 6 residues processed: 130 average time/residue: 1.4554 time to fit residues: 198.4843 Evaluate side-chains 131 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 117 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 414 LYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 414 LYS Chi-restraints excluded: chain B residue 415 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 72 optimal weight: 0.0570 chunk 49 optimal weight: 1.9990 overall best weight: 0.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1288 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= 0.188 Angle : 0.574 5.212 10590 Z= 0.298 Chirality : 0.040 0.136 1254 Planarity : 0.004 0.040 1222 Dihedral : 13.917 114.854 1668 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.04 % Allowed : 13.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.27), residues: 910 helix: 2.32 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.52 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 527 HIS 0.003 0.001 HIS A 200 PHE 0.012 0.001 PHE A 196 TYR 0.019 0.002 TYR A 73 ARG 0.003 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 131 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 0.920 Fit side-chains REVERT: A 49 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7140 (tt) REVERT: A 179 LYS cc_start: 0.5628 (OUTLIER) cc_final: 0.5206 (pptt) REVERT: A 414 LYS cc_start: 0.6070 (OUTLIER) cc_final: 0.5048 (tmtm) REVERT: A 442 ARG cc_start: 0.7141 (ptt-90) cc_final: 0.5917 (ptm160) REVERT: A 478 ARG cc_start: 0.7352 (mtm-85) cc_final: 0.6735 (mtm-85) REVERT: A 489 GLN cc_start: 0.6299 (mm-40) cc_final: 0.5975 (mm-40) REVERT: B 49 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7137 (tt) REVERT: B 179 LYS cc_start: 0.5619 (OUTLIER) cc_final: 0.5197 (pptt) REVERT: B 414 LYS cc_start: 0.6074 (OUTLIER) cc_final: 0.5048 (tmtm) REVERT: B 442 ARG cc_start: 0.7141 (ptt-90) cc_final: 0.5918 (ptm160) REVERT: B 478 ARG cc_start: 0.7351 (mtm-85) cc_final: 0.6735 (mtm-85) REVERT: B 489 GLN cc_start: 0.6301 (mm-40) cc_final: 0.5978 (mm-40) outliers start: 16 outliers final: 6 residues processed: 121 average time/residue: 1.5677 time to fit residues: 198.8630 Evaluate side-chains 127 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 414 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 414 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 78 optimal weight: 50.0000 chunk 21 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 0.0980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7802 Z= 0.160 Angle : 0.536 5.040 10590 Z= 0.279 Chirality : 0.038 0.125 1254 Planarity : 0.004 0.039 1222 Dihedral : 13.158 113.469 1664 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.65 % Allowed : 13.87 % 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: 2.47 (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 0.007 0.001 TRP B 186 HIS 0.003 0.001 HIS A 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 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 124 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 113 time to evaluate : 0.840 Fit side-chains REVERT: A 49 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7129 (tt) REVERT: A 61 PHE cc_start: 0.6569 (m-10) cc_final: 0.5885 (t80) REVERT: A 179 LYS cc_start: 0.5604 (OUTLIER) cc_final: 0.5299 (pmtt) REVERT: A 442 ARG cc_start: 0.7128 (ptt-90) cc_final: 0.5903 (ptm160) REVERT: A 478 ARG cc_start: 0.7371 (mtm-85) cc_final: 0.6815 (mtp180) REVERT: A 489 GLN cc_start: 0.6246 (mm-40) cc_final: 0.5930 (mm-40) REVERT: B 49 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7127 (tt) REVERT: B 61 PHE cc_start: 0.6594 (m-10) cc_final: 0.5900 (t80) REVERT: B 179 LYS cc_start: 0.5594 (OUTLIER) cc_final: 0.5294 (pmtt) REVERT: B 442 ARG cc_start: 0.7127 (ptt-90) cc_final: 0.5904 (ptm160) REVERT: B 478 ARG cc_start: 0.7365 (mtm-85) cc_final: 0.6811 (mtp180) REVERT: B 489 GLN cc_start: 0.6235 (mm-40) cc_final: 0.5918 (mm-40) outliers start: 11 outliers final: 4 residues processed: 118 average time/residue: 1.5128 time to fit residues: 187.3263 Evaluate side-chains 121 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 113 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 83 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 49 optimal weight: 0.0170 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 480 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7802 Z= 0.144 Angle : 0.511 4.933 10590 Z= 0.267 Chirality : 0.037 0.121 1254 Planarity : 0.004 0.038 1222 Dihedral : 12.365 111.097 1652 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.16 % Allowed : 13.36 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.63 (0.27), residues: 910 helix: 2.59 (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 0.007 0.001 TRP A 186 HIS 0.002 0.001 HIS B 200 PHE 0.012 0.001 PHE A 196 TYR 0.016 0.002 TYR B 195 ARG 0.002 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 128 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 113 time to evaluate : 0.941 Fit side-chains REVERT: A 49 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7084 (tt) REVERT: A 61 PHE cc_start: 0.6573 (m-10) cc_final: 0.5885 (t80) REVERT: A 179 LYS cc_start: 0.5566 (OUTLIER) cc_final: 0.5288 (pmtt) REVERT: A 442 ARG cc_start: 0.7113 (ptt-90) cc_final: 0.5909 (ptm160) REVERT: A 478 ARG cc_start: 0.7354 (mtm-85) cc_final: 0.6800 (mtp180) REVERT: A 489 GLN cc_start: 0.6224 (OUTLIER) cc_final: 0.5925 (mm-40) REVERT: B 49 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7080 (tt) REVERT: B 61 PHE cc_start: 0.6588 (m-10) cc_final: 0.5881 (t80) REVERT: B 179 LYS cc_start: 0.5561 (OUTLIER) cc_final: 0.5285 (pmtt) REVERT: B 442 ARG cc_start: 0.7118 (ptt-90) cc_final: 0.5911 (ptm160) REVERT: B 478 ARG cc_start: 0.7354 (mtm-85) cc_final: 0.6801 (mtp180) REVERT: B 489 GLN cc_start: 0.6222 (OUTLIER) cc_final: 0.5924 (mm-40) outliers start: 15 outliers final: 4 residues processed: 119 average time/residue: 1.5775 time to fit residues: 197.2847 Evaluate side-chains 123 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 489 GLN Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 489 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.9990 chunk 49 optimal weight: 0.0670 chunk 73 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 51 optimal weight: 0.0970 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7802 Z= 0.136 Angle : 0.502 4.934 10590 Z= 0.263 Chirality : 0.037 0.121 1254 Planarity : 0.004 0.037 1222 Dihedral : 12.068 109.133 1652 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.04 % Allowed : 13.49 % 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: 2.70 (0.27), residues: 910 helix: 2.66 (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 0.007 0.001 TRP B 186 HIS 0.002 0.001 HIS A 200 PHE 0.012 0.001 PHE A 196 TYR 0.016 0.002 TYR B 195 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 129 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 115 time to evaluate : 0.857 Fit side-chains REVERT: A 49 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7076 (tt) REVERT: A 61 PHE cc_start: 0.6574 (m-10) cc_final: 0.5847 (t80) REVERT: A 179 LYS cc_start: 0.5567 (OUTLIER) cc_final: 0.5255 (pmtt) REVERT: A 183 ARG cc_start: 0.6663 (ttp-170) cc_final: 0.6344 (ttm170) REVERT: A 442 ARG cc_start: 0.7100 (ptt-90) cc_final: 0.5899 (ptm160) REVERT: A 478 ARG cc_start: 0.7346 (mtm-85) cc_final: 0.6786 (mtp180) REVERT: A 489 GLN cc_start: 0.6169 (OUTLIER) cc_final: 0.5873 (mm-40) REVERT: B 49 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7067 (tt) REVERT: B 61 PHE cc_start: 0.6583 (m-10) cc_final: 0.5872 (t80) REVERT: B 179 LYS cc_start: 0.5564 (OUTLIER) cc_final: 0.5255 (pmtt) REVERT: B 183 ARG cc_start: 0.6659 (ttp-170) cc_final: 0.6340 (ttm170) REVERT: B 442 ARG cc_start: 0.7099 (ptt-90) cc_final: 0.5900 (ptm160) REVERT: B 478 ARG cc_start: 0.7344 (mtm-85) cc_final: 0.6784 (mtp180) REVERT: B 489 GLN cc_start: 0.6169 (OUTLIER) cc_final: 0.5873 (mm-40) outliers start: 14 outliers final: 4 residues processed: 123 average time/residue: 1.4347 time to fit residues: 185.3325 Evaluate side-chains 123 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 489 GLN Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 489 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 8 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 78 optimal weight: 50.0000 chunk 83 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1487 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= 0.165 Angle : 0.542 4.971 10590 Z= 0.282 Chirality : 0.038 0.125 1254 Planarity : 0.004 0.038 1222 Dihedral : 12.372 110.701 1652 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.04 % Allowed : 13.10 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.55 (0.27), residues: 910 helix: 2.52 (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 0.003 0.001 HIS A 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 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 fitting. rotamer outliers: 14 poor density : 116 time to evaluate : 0.843 Fit side-chains REVERT: A 49 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7105 (tt) REVERT: A 61 PHE cc_start: 0.6645 (m-10) cc_final: 0.5906 (t80) REVERT: A 179 LYS cc_start: 0.5615 (OUTLIER) cc_final: 0.5292 (pmtt) REVERT: A 442 ARG cc_start: 0.7124 (ptt-90) cc_final: 0.5907 (ptm160) REVERT: A 478 ARG cc_start: 0.7360 (mtm-85) cc_final: 0.6786 (mtp180) REVERT: A 489 GLN cc_start: 0.6252 (OUTLIER) cc_final: 0.5944 (mm-40) REVERT: B 49 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7117 (tt) REVERT: B 61 PHE cc_start: 0.6630 (m-10) cc_final: 0.5899 (t80) REVERT: B 179 LYS cc_start: 0.5614 (OUTLIER) cc_final: 0.5292 (pmtt) REVERT: B 442 ARG cc_start: 0.7126 (ptt-90) cc_final: 0.5909 (ptm160) REVERT: B 478 ARG cc_start: 0.7359 (mtm-85) cc_final: 0.6785 (mtp180) REVERT: B 489 GLN cc_start: 0.6252 (OUTLIER) cc_final: 0.5944 (mm-40) outliers start: 14 outliers final: 4 residues processed: 121 average time/residue: 1.4446 time to fit residues: 183.4346 Evaluate side-chains 126 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 116 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 489 GLN Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 489 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 85 optimal weight: 0.0060 chunk 52 optimal weight: 3.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1552 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= 0.151 Angle : 0.524 4.948 10590 Z= 0.273 Chirality : 0.038 0.124 1254 Planarity : 0.004 0.037 1222 Dihedral : 12.286 110.962 1652 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.78 % Allowed : 13.36 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.63 (0.27), residues: 910 helix: 2.59 (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 A 200 PHE 0.012 0.001 PHE A 196 TYR 0.017 0.002 TYR B 195 ARG 0.002 0.000 ARG A 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 127 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 0.782 Fit side-chains REVERT: A 49 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7103 (tt) REVERT: A 61 PHE cc_start: 0.6642 (m-10) cc_final: 0.5897 (t80) REVERT: A 179 LYS cc_start: 0.5608 (OUTLIER) cc_final: 0.5288 (pmtt) REVERT: A 442 ARG cc_start: 0.7115 (ptt-90) cc_final: 0.5896 (ptm160) REVERT: A 478 ARG cc_start: 0.7359 (mtm-85) cc_final: 0.6787 (mtp180) REVERT: A 489 GLN cc_start: 0.6199 (OUTLIER) cc_final: 0.5898 (mm-40) REVERT: B 49 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7099 (tt) REVERT: B 61 PHE cc_start: 0.6632 (m-10) cc_final: 0.5894 (t80) REVERT: B 179 LYS cc_start: 0.5607 (OUTLIER) cc_final: 0.5288 (pmtt) REVERT: B 442 ARG cc_start: 0.7114 (ptt-90) cc_final: 0.5897 (ptm160) REVERT: B 478 ARG cc_start: 0.7357 (mtm-85) cc_final: 0.6785 (mtp180) REVERT: B 489 GLN cc_start: 0.6199 (OUTLIER) cc_final: 0.5899 (mm-40) outliers start: 12 outliers final: 4 residues processed: 121 average time/residue: 1.5253 time to fit residues: 193.3806 Evaluate side-chains 125 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 489 GLN Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 489 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7802 Z= 0.227 Angle : 0.609 5.195 10590 Z= 0.313 Chirality : 0.041 0.137 1254 Planarity : 0.004 0.040 1222 Dihedral : 12.882 113.171 1652 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.04 % Allowed : 13.10 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.32 (0.27), residues: 910 helix: 2.33 (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 0.007 0.002 TRP B 498 HIS 0.004 0.002 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 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 127 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 113 time to evaluate : 0.823 Fit side-chains REVERT: A 49 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7170 (tt) REVERT: A 61 PHE cc_start: 0.6702 (m-10) cc_final: 0.5942 (t80) REVERT: A 179 LYS cc_start: 0.5649 (OUTLIER) cc_final: 0.5308 (pmtt) REVERT: A 442 ARG cc_start: 0.7138 (ptt-90) cc_final: 0.5925 (ptm160) REVERT: A 478 ARG cc_start: 0.7389 (mtm-85) cc_final: 0.6746 (mtp180) REVERT: A 489 GLN cc_start: 0.6286 (OUTLIER) cc_final: 0.5961 (mm-40) REVERT: B 49 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7176 (tt) REVERT: B 61 PHE cc_start: 0.6705 (m-10) cc_final: 0.5935 (t80) REVERT: B 179 LYS cc_start: 0.5647 (OUTLIER) cc_final: 0.5307 (pmtt) REVERT: B 442 ARG cc_start: 0.7138 (ptt-90) cc_final: 0.5926 (ptm160) REVERT: B 478 ARG cc_start: 0.7386 (mtm-85) cc_final: 0.6746 (mtp180) REVERT: B 489 GLN cc_start: 0.6317 (OUTLIER) cc_final: 0.5988 (mm-40) outliers start: 14 outliers final: 4 residues processed: 117 average time/residue: 1.4870 time to fit residues: 182.4654 Evaluate side-chains 123 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 489 GLN Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 489 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 0.0980 chunk 51 optimal weight: 0.0770 overall best weight: 0.5740 ------------------------------------------------------------------------------- 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 = 0.3394 r_free = 0.3394 target = 0.130020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.093851 restraints weight = 9187.005| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.41 r_work: 0.2786 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1568 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= 0.141 Angle : 0.516 4.944 10590 Z= 0.269 Chirality : 0.037 0.122 1254 Planarity : 0.004 0.037 1222 Dihedral : 12.441 112.774 1652 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.78 % Allowed : 13.36 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.61 (0.27), residues: 910 helix: 2.58 (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 0.008 0.001 TRP A 186 HIS 0.002 0.001 HIS B 200 PHE 0.012 0.001 PHE A 196 TYR 0.016 0.002 TYR B 195 ARG 0.002 0.000 ARG A 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4049.06 seconds wall clock time: 71 minutes 27.96 seconds (4287.96 seconds total)