Starting phenix.real_space_refine on Fri Jul 19 06:36:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8teo_41193/07_2024/8teo_41193.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8teo_41193/07_2024/8teo_41193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8teo_41193/07_2024/8teo_41193.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8teo_41193/07_2024/8teo_41193.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8teo_41193/07_2024/8teo_41193.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8teo_41193/07_2024/8teo_41193.cif" } resolution = 2.39 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= 0.001 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: 5 Type Number sf(0) Gaussians K 2 8.98 5 S 28 5.16 5 C 4488 2.51 5 N 960 2.21 5 O 1029 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 6507 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1536 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1536 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1536 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1536 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 90 Unusual residues: {' K': 2, 'POV': 8} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-3': 6, 'POV:plan-2': 6, 'POV:plan-1': 7} Unresolved non-hydrogen planarities: 67 Chain: "B" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 88 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-3': 6, 'POV:plan-2': 6, 'POV:plan-1': 7} Unresolved non-hydrogen planarities: 67 Chain: "C" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 88 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-3': 6, 'POV:plan-2': 6, 'POV:plan-1': 7} Unresolved non-hydrogen planarities: 67 Chain: "D" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 88 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-3': 6, 'POV:plan-2': 6, 'POV:plan-1': 7} Unresolved non-hydrogen planarities: 67 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 4.73, per 1000 atoms: 0.73 Number of scatterers: 6507 At special positions: 0 Unit cell: (105.41, 105.41, 64.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 2 19.00 S 28 16.00 O 1029 8.00 N 960 7.00 C 4488 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.73 Conformation dependent library (CDL) restraints added in 1.1 seconds 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1480 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 86.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 226 through 248 Processing helix chain 'A' and resid 279 through 298 Processing helix chain 'A' and resid 311 through 319 Processing helix chain 'A' and resid 320 through 326 Processing helix chain 'A' and resid 358 through 368 Processing helix chain 'A' and resid 369 through 377 Processing helix chain 'A' and resid 380 through 392 Processing helix chain 'A' and resid 392 through 419 Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 432 through 441 Processing helix chain 'A' and resid 452 through 472 Processing helix chain 'A' and resid 473 through 489 removed outlier: 4.123A pdb=" N ILE A 477 " --> pdb=" O PRO A 473 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N SER A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 248 Processing helix chain 'B' and resid 279 through 298 Processing helix chain 'B' and resid 311 through 319 Processing helix chain 'B' and resid 320 through 326 Processing helix chain 'B' and resid 358 through 368 Processing helix chain 'B' and resid 369 through 377 Processing helix chain 'B' and resid 380 through 392 Processing helix chain 'B' and resid 392 through 419 Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 432 through 441 Processing helix chain 'B' and resid 452 through 472 Processing helix chain 'B' and resid 473 through 489 removed outlier: 4.123A pdb=" N ILE B 477 " --> pdb=" O PRO B 473 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N SER B 479 " --> pdb=" O PRO B 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 248 Processing helix chain 'C' and resid 279 through 298 Processing helix chain 'C' and resid 311 through 319 Processing helix chain 'C' and resid 320 through 326 Processing helix chain 'C' and resid 358 through 368 Processing helix chain 'C' and resid 369 through 377 Processing helix chain 'C' and resid 380 through 392 Processing helix chain 'C' and resid 392 through 419 Processing helix chain 'C' and resid 429 through 431 No H-bonds generated for 'chain 'C' and resid 429 through 431' Processing helix chain 'C' and resid 432 through 441 Processing helix chain 'C' and resid 452 through 472 Processing helix chain 'C' and resid 473 through 489 removed outlier: 4.123A pdb=" N ILE C 477 " --> pdb=" O PRO C 473 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N SER C 479 " --> pdb=" O PRO C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 248 Processing helix chain 'D' and resid 279 through 298 Processing helix chain 'D' and resid 311 through 319 Processing helix chain 'D' and resid 320 through 326 Processing helix chain 'D' and resid 358 through 368 Processing helix chain 'D' and resid 369 through 377 Processing helix chain 'D' and resid 380 through 392 Processing helix chain 'D' and resid 392 through 419 Processing helix chain 'D' and resid 429 through 431 No H-bonds generated for 'chain 'D' and resid 429 through 431' Processing helix chain 'D' and resid 432 through 441 Processing helix chain 'D' and resid 452 through 472 Processing helix chain 'D' and resid 473 through 489 removed outlier: 4.124A pdb=" N ILE D 477 " --> pdb=" O PRO D 473 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N SER D 479 " --> pdb=" O PRO D 475 " (cutoff:3.500A) 489 hydrogen bonds defined for protein. 1395 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.78 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 888 1.31 - 1.43: 1808 1.43 - 1.56: 3788 1.56 - 1.68: 84 1.68 - 1.81: 44 Bond restraints: 6612 Sorted by residual: bond pdb=" C31 POV A 701 " pdb=" O31 POV A 701 " ideal model delta sigma weight residual 1.327 1.442 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C31 POV D 704 " pdb=" O31 POV D 704 " ideal model delta sigma weight residual 1.327 1.442 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C31 POV B 703 " pdb=" O31 POV B 703 " ideal model delta sigma weight residual 1.327 1.442 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C31 POV C 702 " pdb=" O31 POV C 702 " ideal model delta sigma weight residual 1.327 1.442 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C31 POV C 701 " pdb=" O31 POV C 701 " ideal model delta sigma weight residual 1.327 1.440 -0.113 2.00e-02 2.50e+03 3.17e+01 ... (remaining 6607 not shown) Histogram of bond angle deviations from ideal: 100.46 - 107.17: 160 107.17 - 113.88: 4026 113.88 - 120.58: 2570 120.58 - 127.29: 2056 127.29 - 133.99: 56 Bond angle restraints: 8868 Sorted by residual: angle pdb=" C32 POV B 708 " pdb=" C31 POV B 708 " pdb=" O31 POV B 708 " ideal model delta sigma weight residual 110.66 120.30 -9.64 3.00e+00 1.11e-01 1.03e+01 angle pdb=" C32 POV D 703 " pdb=" C31 POV D 703 " pdb=" O31 POV D 703 " ideal model delta sigma weight residual 110.66 120.30 -9.64 3.00e+00 1.11e-01 1.03e+01 angle pdb=" C32 POV C 701 " pdb=" C31 POV C 701 " pdb=" O31 POV C 701 " ideal model delta sigma weight residual 110.66 120.26 -9.60 3.00e+00 1.11e-01 1.03e+01 angle pdb=" C32 POV B 703 " pdb=" C31 POV B 703 " pdb=" O31 POV B 703 " ideal model delta sigma weight residual 110.66 120.26 -9.60 3.00e+00 1.11e-01 1.02e+01 angle pdb=" C32 POV D 704 " pdb=" C31 POV D 704 " pdb=" O31 POV D 704 " ideal model delta sigma weight residual 110.66 120.26 -9.60 3.00e+00 1.11e-01 1.02e+01 ... (remaining 8863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.01: 3524 23.01 - 46.02: 256 46.02 - 69.03: 60 69.03 - 92.04: 0 92.04 - 115.05: 4 Dihedral angle restraints: 3844 sinusoidal: 1576 harmonic: 2268 Sorted by residual: dihedral pdb=" C3 POV C 702 " pdb=" C31 POV C 702 " pdb=" O31 POV C 702 " pdb=" C32 POV C 702 " ideal model delta sinusoidal sigma weight residual 172.61 57.56 115.05 1 3.00e+01 1.11e-03 1.52e+01 dihedral pdb=" C3 POV B 703 " pdb=" C31 POV B 703 " pdb=" O31 POV B 703 " pdb=" C32 POV B 703 " ideal model delta sinusoidal sigma weight residual 172.61 57.58 115.03 1 3.00e+01 1.11e-03 1.52e+01 dihedral pdb=" C3 POV D 704 " pdb=" C31 POV D 704 " pdb=" O31 POV D 704 " pdb=" C32 POV D 704 " ideal model delta sinusoidal sigma weight residual 172.61 57.58 115.03 1 3.00e+01 1.11e-03 1.52e+01 ... (remaining 3841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 776 0.038 - 0.075: 226 0.075 - 0.113: 52 0.113 - 0.151: 13 0.151 - 0.188: 5 Chirality restraints: 1072 Sorted by residual: chirality pdb=" CA LEU B 472 " pdb=" N LEU B 472 " pdb=" C LEU B 472 " pdb=" CB LEU B 472 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.85e-01 chirality pdb=" CA LEU C 472 " pdb=" N LEU C 472 " pdb=" C LEU C 472 " pdb=" CB LEU C 472 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.77e-01 chirality pdb=" CA LEU D 472 " pdb=" N LEU D 472 " pdb=" C LEU D 472 " pdb=" CB LEU D 472 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.74e-01 ... (remaining 1069 not shown) Planarity restraints: 1020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 472 " -0.055 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO D 473 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO D 473 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 473 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 472 " 0.055 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO A 473 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 473 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 473 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 472 " -0.055 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO B 473 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO B 473 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 473 " -0.046 5.00e-02 4.00e+02 ... (remaining 1017 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.84: 2061 2.84 - 3.41: 7234 3.41 - 3.99: 12345 3.99 - 4.56: 17852 4.56 - 5.14: 25567 Nonbonded interactions: 65059 Sorted by model distance: nonbonded pdb=" OE2 GLU A 283 " pdb=" NH2 ARG A 371 " model vdw 2.259 2.520 nonbonded pdb=" OE2 GLU B 283 " pdb=" NH2 ARG B 371 " model vdw 2.260 2.520 nonbonded pdb=" OE2 GLU D 283 " pdb=" NH2 ARG D 371 " model vdw 2.260 2.520 nonbonded pdb=" OE2 GLU C 283 " pdb=" NH2 ARG C 371 " model vdw 2.260 2.520 nonbonded pdb=" OE2 GLU C 283 " pdb=" NH1 ARG C 368 " model vdw 2.272 2.520 ... (remaining 65054 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 226 through 489 or (resid 702 and (name C31 or name C32 or \ name C33 or name C34 or name C35)) or (resid 703 through 704 and (name C32 or n \ ame C33 or name C34 or name C35)))) selection = (chain 'B' and (resid 226 through 489 or (resid 702 and (name C31 or name C32 or \ name C33 or name C34 or name C35)) or (resid 703 through 704 and (name C32 or n \ ame C33 or name C34 or name C35)))) selection = (chain 'C' and (resid 226 through 489 or (resid 702 and (name C31 or name C32 or \ name C33 or name C34 or name C35)) or (resid 703 through 704 and (name C32 or n \ ame C33 or name C34 or name C35)))) selection = (chain 'D' and (resid 226 through 489 or (resid 702 and (name C31 or name C32 or \ name C33 or name C34 or name C35)) or (resid 703 through 704 and (name C32 or n \ ame C33 or name C34 or name C35)))) } 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=1.00 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: 1.130 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: 0.080 Process input model: 22.540 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:16.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 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 : 0.009 0.115 6612 Z= 0.614 Angle : 0.967 9.640 8868 Z= 0.399 Chirality : 0.041 0.188 1072 Planarity : 0.008 0.083 1020 Dihedral : 16.683 115.049 2364 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.60 % Allowed : 5.42 % Favored : 93.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.20 (0.31), residues: 752 helix: 1.79 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -0.48 (0.65), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 289 HIS 0.002 0.001 HIS B 486 PHE 0.033 0.002 PHE A 433 TYR 0.008 0.001 TYR B 415 ARG 0.008 0.001 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 110 time to evaluate : 0.694 Fit side-chains outliers start: 4 outliers final: 8 residues processed: 114 average time/residue: 1.3885 time to fit residues: 165.0927 Evaluate side-chains 112 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 231 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 31 optimal weight: 0.2980 chunk 19 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 23 optimal weight: 0.1980 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.8299 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6612 Z= 0.181 Angle : 0.512 5.184 8868 Z= 0.268 Chirality : 0.039 0.133 1072 Planarity : 0.005 0.059 1020 Dihedral : 13.145 73.537 1072 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.75 % Allowed : 7.98 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 3.64 (0.31), residues: 752 helix: 2.85 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.47 (0.59), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 289 HIS 0.002 0.001 HIS D 486 PHE 0.026 0.002 PHE C 433 TYR 0.009 0.001 TYR C 323 ARG 0.005 0.001 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 119 time to evaluate : 0.707 Fit side-chains REVERT: A 390 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8428 (tttm) REVERT: A 487 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.6991 (ttp-170) REVERT: B 487 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.6955 (ttp-170) REVERT: C 487 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.6980 (ttp-170) REVERT: D 487 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.6975 (ttp-170) outliers start: 5 outliers final: 4 residues processed: 119 average time/residue: 1.5687 time to fit residues: 193.7607 Evaluate side-chains 117 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 108 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 487 ARG Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 487 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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: 0.8397 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 6612 Z= 0.300 Angle : 0.572 5.973 8868 Z= 0.300 Chirality : 0.043 0.149 1072 Planarity : 0.004 0.037 1020 Dihedral : 11.685 67.324 1068 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.36 % Allowed : 9.79 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 3.28 (0.32), residues: 752 helix: 2.55 (0.21), residues: 608 sheet: None (None), residues: 0 loop : 0.53 (0.62), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 289 HIS 0.003 0.002 HIS D 378 PHE 0.021 0.002 PHE A 433 TYR 0.008 0.002 TYR A 323 ARG 0.004 0.001 ARG D 362 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 127 time to evaluate : 0.718 Fit side-chains REVERT: A 390 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8408 (tttm) REVERT: A 395 GLU cc_start: 0.8285 (mp0) cc_final: 0.8085 (mp0) REVERT: A 487 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.6984 (ttp-170) REVERT: B 487 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.6949 (ttp-170) REVERT: C 487 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.6967 (ttp-170) REVERT: D 487 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.6953 (ttp-170) outliers start: 9 outliers final: 6 residues processed: 131 average time/residue: 1.1815 time to fit residues: 162.4088 Evaluate side-chains 125 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 114 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 487 ARG Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 487 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6612 Z= 0.176 Angle : 0.479 4.946 8868 Z= 0.252 Chirality : 0.039 0.139 1072 Planarity : 0.004 0.035 1020 Dihedral : 9.990 56.358 1068 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.51 % Allowed : 13.10 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 3.39 (0.32), residues: 752 helix: 2.66 (0.21), residues: 624 sheet: None (None), residues: 0 loop : 0.07 (0.63), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 289 HIS 0.002 0.001 HIS A 378 PHE 0.021 0.001 PHE A 244 TYR 0.006 0.001 TYR B 485 ARG 0.004 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 123 time to evaluate : 0.738 Fit side-chains REVERT: A 395 GLU cc_start: 0.8199 (mp0) cc_final: 0.7882 (mp0) REVERT: A 487 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.6949 (ttp-170) REVERT: B 487 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.6931 (ttp-170) REVERT: C 395 GLU cc_start: 0.8192 (mp0) cc_final: 0.7894 (mp0) REVERT: C 487 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.6964 (ttp-170) REVERT: D 395 GLU cc_start: 0.8192 (mp0) cc_final: 0.7892 (mp0) REVERT: D 487 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.6942 (ttp-170) outliers start: 10 outliers final: 3 residues processed: 127 average time/residue: 1.1076 time to fit residues: 148.1436 Evaluate side-chains 117 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 110 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 487 ARG Chi-restraints excluded: chain D residue 487 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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: 0.8422 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 6612 Z= 0.362 Angle : 0.579 6.810 8868 Z= 0.305 Chirality : 0.043 0.153 1072 Planarity : 0.004 0.032 1020 Dihedral : 10.597 56.425 1066 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.56 % Allowed : 13.70 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 3.30 (0.32), residues: 752 helix: 2.52 (0.21), residues: 608 sheet: None (None), residues: 0 loop : 0.77 (0.62), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 454 HIS 0.003 0.002 HIS A 486 PHE 0.020 0.002 PHE C 244 TYR 0.009 0.002 TYR D 485 ARG 0.003 0.001 ARG D 365 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 104 time to evaluate : 0.682 Fit side-chains REVERT: A 395 GLU cc_start: 0.8236 (mp0) cc_final: 0.7972 (mp0) REVERT: A 487 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.6975 (ttp-170) REVERT: B 487 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.6965 (ttp-170) REVERT: C 395 GLU cc_start: 0.8233 (mp0) cc_final: 0.7969 (mp0) REVERT: C 487 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.6973 (ttp-170) REVERT: D 395 GLU cc_start: 0.8235 (mp0) cc_final: 0.7968 (mp0) REVERT: D 487 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.6970 (ttp-170) outliers start: 17 outliers final: 5 residues processed: 115 average time/residue: 1.2964 time to fit residues: 156.0249 Evaluate side-chains 115 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 106 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 487 ARG Chi-restraints excluded: chain D residue 487 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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: 0.8387 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6612 Z= 0.202 Angle : 0.489 5.518 8868 Z= 0.259 Chirality : 0.039 0.144 1072 Planarity : 0.004 0.031 1020 Dihedral : 9.461 57.785 1066 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.51 % Allowed : 14.61 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 3.40 (0.32), residues: 752 helix: 2.59 (0.21), residues: 624 sheet: None (None), residues: 0 loop : 0.49 (0.65), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 454 HIS 0.002 0.001 HIS B 378 PHE 0.022 0.001 PHE C 244 TYR 0.006 0.001 TYR D 485 ARG 0.003 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 0.758 Fit side-chains REVERT: A 395 GLU cc_start: 0.8242 (mp0) cc_final: 0.7910 (mp0) REVERT: A 487 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.6964 (ttp-170) REVERT: B 487 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.6953 (ttp-170) REVERT: C 380 LYS cc_start: 0.8353 (tppp) cc_final: 0.7889 (tptp) REVERT: C 395 GLU cc_start: 0.8241 (mp0) cc_final: 0.7894 (mp0) REVERT: C 487 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.6960 (ttp-170) REVERT: D 395 GLU cc_start: 0.8241 (mp0) cc_final: 0.7898 (mp0) REVERT: D 487 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.6959 (ttp-170) outliers start: 10 outliers final: 4 residues processed: 115 average time/residue: 1.3466 time to fit residues: 162.4790 Evaluate side-chains 114 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 106 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 487 ARG Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 487 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.8377 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6612 Z= 0.184 Angle : 0.476 5.191 8868 Z= 0.250 Chirality : 0.038 0.139 1072 Planarity : 0.004 0.026 1020 Dihedral : 8.647 58.582 1062 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.51 % Allowed : 14.76 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 3.48 (0.32), residues: 752 helix: 2.65 (0.21), residues: 624 sheet: None (None), residues: 0 loop : 0.55 (0.65), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 454 HIS 0.002 0.001 HIS D 378 PHE 0.022 0.001 PHE B 244 TYR 0.006 0.001 TYR B 485 ARG 0.003 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 0.761 Fit side-chains REVERT: A 395 GLU cc_start: 0.8208 (mp0) cc_final: 0.7938 (mp0) REVERT: A 487 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.6954 (ttp-170) REVERT: B 487 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.6957 (ttp-170) REVERT: C 380 LYS cc_start: 0.8350 (tppp) cc_final: 0.7864 (tptp) REVERT: C 395 GLU cc_start: 0.8205 (mp0) cc_final: 0.7947 (mp0) REVERT: C 487 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.6960 (ttp-170) REVERT: D 395 GLU cc_start: 0.8206 (mp0) cc_final: 0.7945 (mp0) REVERT: D 487 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.6959 (ttp-170) outliers start: 10 outliers final: 8 residues processed: 112 average time/residue: 1.4048 time to fit residues: 164.2927 Evaluate side-chains 119 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 107 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 487 ARG Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 487 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 70 optimal weight: 0.2980 chunk 64 optimal weight: 0.3980 chunk 68 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.8360 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6612 Z= 0.154 Angle : 0.455 4.983 8868 Z= 0.239 Chirality : 0.038 0.136 1072 Planarity : 0.004 0.028 1020 Dihedral : 8.066 59.401 1062 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.36 % Allowed : 15.21 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 3.58 (0.32), residues: 752 helix: 2.73 (0.21), residues: 624 sheet: None (None), residues: 0 loop : 0.53 (0.65), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 454 HIS 0.001 0.001 HIS A 378 PHE 0.021 0.001 PHE A 244 TYR 0.006 0.001 TYR A 485 ARG 0.003 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 110 time to evaluate : 0.699 Fit side-chains REVERT: A 247 GLU cc_start: 0.7817 (pt0) cc_final: 0.7542 (pt0) REVERT: A 395 GLU cc_start: 0.8201 (mp0) cc_final: 0.7950 (mp0) REVERT: A 487 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.6971 (ttp-170) REVERT: B 487 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.6947 (ttp-170) REVERT: C 395 GLU cc_start: 0.8205 (mp0) cc_final: 0.7965 (mp0) REVERT: C 487 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.6969 (ttp-170) REVERT: D 395 GLU cc_start: 0.8206 (mp0) cc_final: 0.7966 (mp0) REVERT: D 487 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.6968 (ttp-170) outliers start: 9 outliers final: 6 residues processed: 113 average time/residue: 1.3377 time to fit residues: 158.0661 Evaluate side-chains 119 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 487 ARG Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 487 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 72 optimal weight: 0.0870 chunk 34 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 overall best weight: 0.6760 ------------------------------------------------------------------------------- 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: 0.8366 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6612 Z= 0.165 Angle : 0.461 5.051 8868 Z= 0.242 Chirality : 0.038 0.137 1072 Planarity : 0.003 0.025 1020 Dihedral : 7.886 59.235 1062 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.26 % Allowed : 14.31 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 3.56 (0.32), residues: 752 helix: 2.70 (0.21), residues: 624 sheet: None (None), residues: 0 loop : 0.58 (0.65), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 454 HIS 0.001 0.001 HIS D 378 PHE 0.020 0.001 PHE A 244 TYR 0.006 0.001 TYR B 485 ARG 0.003 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 0.666 Fit side-chains REVERT: A 247 GLU cc_start: 0.7828 (pt0) cc_final: 0.7561 (pt0) REVERT: A 395 GLU cc_start: 0.8202 (mp0) cc_final: 0.7963 (mp0) REVERT: A 487 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.6957 (ttp-170) REVERT: B 487 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.6945 (ttp-170) REVERT: C 380 LYS cc_start: 0.8349 (tppp) cc_final: 0.7858 (tptp) REVERT: C 395 GLU cc_start: 0.8201 (mp0) cc_final: 0.7943 (mp0) REVERT: C 487 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.6974 (ttp-170) REVERT: D 395 GLU cc_start: 0.8201 (mp0) cc_final: 0.7941 (mp0) REVERT: D 487 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.6966 (ttp-170) outliers start: 15 outliers final: 9 residues processed: 117 average time/residue: 1.2732 time to fit residues: 155.5754 Evaluate side-chains 122 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 487 ARG Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 487 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 64 optimal weight: 0.0670 chunk 18 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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: 0.8361 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6612 Z= 0.157 Angle : 0.454 4.981 8868 Z= 0.238 Chirality : 0.038 0.136 1072 Planarity : 0.003 0.028 1020 Dihedral : 7.724 59.474 1062 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.81 % Allowed : 14.76 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 3.62 (0.32), residues: 752 helix: 2.75 (0.21), residues: 624 sheet: None (None), residues: 0 loop : 0.58 (0.65), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 454 HIS 0.001 0.001 HIS D 378 PHE 0.020 0.001 PHE A 244 TYR 0.007 0.001 TYR A 485 ARG 0.003 0.000 ARG A 362 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 0.647 Fit side-chains REVERT: A 247 GLU cc_start: 0.7808 (pt0) cc_final: 0.7547 (pt0) REVERT: A 380 LYS cc_start: 0.8350 (tppp) cc_final: 0.7875 (tptp) REVERT: A 395 GLU cc_start: 0.8207 (mp0) cc_final: 0.7957 (mp0) REVERT: A 487 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.6953 (ttp-170) REVERT: B 380 LYS cc_start: 0.8343 (tppp) cc_final: 0.7876 (tptp) REVERT: B 487 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.6963 (ttp-170) REVERT: C 380 LYS cc_start: 0.8348 (tppp) cc_final: 0.7872 (tptp) REVERT: C 395 GLU cc_start: 0.8206 (mp0) cc_final: 0.7963 (mp0) REVERT: C 487 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.6962 (ttp-170) REVERT: D 380 LYS cc_start: 0.8343 (tppp) cc_final: 0.7875 (tptp) REVERT: D 395 GLU cc_start: 0.8206 (mp0) cc_final: 0.7963 (mp0) REVERT: D 487 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.6981 (ttp-170) outliers start: 12 outliers final: 6 residues processed: 117 average time/residue: 1.2926 time to fit residues: 158.1504 Evaluate side-chains 119 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 487 ARG Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 487 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 43 optimal weight: 0.2980 chunk 69 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3461 r_free = 0.3461 target = 0.122429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.093073 restraints weight = 7153.579| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.71 r_work: 0.2856 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6612 Z= 0.153 Angle : 0.450 5.072 8868 Z= 0.236 Chirality : 0.037 0.136 1072 Planarity : 0.003 0.025 1020 Dihedral : 7.550 59.803 1062 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.36 % Allowed : 15.06 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 3.62 (0.32), residues: 752 helix: 2.74 (0.21), residues: 624 sheet: None (None), residues: 0 loop : 0.62 (0.65), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 454 HIS 0.001 0.001 HIS C 378 PHE 0.020 0.001 PHE A 244 TYR 0.006 0.001 TYR C 485 ARG 0.003 0.000 ARG A 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3027.99 seconds wall clock time: 53 minutes 44.19 seconds (3224.19 seconds total)