Starting phenix.real_space_refine on Mon Mar 11 10:02:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nll_12465/03_2024/7nll_12465_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nll_12465/03_2024/7nll_12465.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nll_12465/03_2024/7nll_12465.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nll_12465/03_2024/7nll_12465.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nll_12465/03_2024/7nll_12465_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nll_12465/03_2024/7nll_12465_updated.pdb" } resolution = 2.89 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 ------------------------------------------------------------------------------- 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= 0.078 sd= 0.125 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2915 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 3220 2.51 5 N 829 2.21 5 O 985 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-5265/modules/chem_data/mon_lib" Total number of atoms: 5056 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1501 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 184} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1494 Classifications: {'peptide': 195} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 183} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1021 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "C" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1012 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'RTV': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'RTV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.46, per 1000 atoms: 0.68 Number of scatterers: 5056 At special positions: 0 Unit cell: (92.92, 57.57, 105.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 985 8.00 N 829 7.00 C 3220 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 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: 1.88 Conformation dependent library (CDL) restraints added in 946.7 milliseconds 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1184 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 16 helices and 8 sheets defined 10.4% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'B' and resid 338 through 342 Processing helix chain 'B' and resid 366 through 369 No H-bonds generated for 'chain 'B' and resid 366 through 369' Processing helix chain 'B' and resid 384 through 387 No H-bonds generated for 'chain 'B' and resid 384 through 387' Processing helix chain 'B' and resid 404 through 409 removed outlier: 4.330A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN B 409 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 409' Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 439 through 442 No H-bonds generated for 'chain 'B' and resid 439 through 442' Processing helix chain 'D' and resid 338 through 342 Processing helix chain 'D' and resid 366 through 369 No H-bonds generated for 'chain 'D' and resid 366 through 369' Processing helix chain 'D' and resid 384 through 387 No H-bonds generated for 'chain 'D' and resid 384 through 387' Processing helix chain 'D' and resid 404 through 409 removed outlier: 4.329A pdb=" N ARG D 408 " --> pdb=" O GLY D 404 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN D 409 " --> pdb=" O ASP D 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 404 through 409' Processing helix chain 'D' and resid 417 through 421 Processing helix chain 'D' and resid 439 through 442 No H-bonds generated for 'chain 'D' and resid 439 through 442' Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing sheet with id= A, first strand: chain 'B' and resid 354 through 358 Processing sheet with id= B, first strand: chain 'B' and resid 452 through 454 Processing sheet with id= C, first strand: chain 'D' and resid 354 through 358 Processing sheet with id= D, first strand: chain 'D' and resid 452 through 454 Processing sheet with id= E, first strand: chain 'A' and resid 3 through 7 Processing sheet with id= F, first strand: chain 'A' and resid 125 through 127 removed outlier: 3.595A pdb=" N SER A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ARG A 38 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N GLY A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 3 through 7 Processing sheet with id= H, first strand: chain 'C' and resid 125 through 127 removed outlier: 3.595A pdb=" N SER C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ARG C 38 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N GLY C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) 126 hydrogen bonds defined for protein. 318 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: 1.25 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1620 1.34 - 1.46: 1413 1.46 - 1.58: 2139 1.58 - 1.70: 0 1.70 - 1.81: 24 Bond restraints: 5196 Sorted by residual: bond pdb=" C5 RTV D1001 " pdb=" O5 RTV D1001 " ideal model delta sigma weight residual 1.411 1.436 -0.025 2.00e-02 2.50e+03 1.52e+00 bond pdb=" C5 RTV B1001 " pdb=" O5 RTV B1001 " ideal model delta sigma weight residual 1.411 1.435 -0.024 2.00e-02 2.50e+03 1.49e+00 bond pdb=" C1 RTV B1001 " pdb=" O5 RTV B1001 " ideal model delta sigma weight residual 1.406 1.428 -0.022 2.00e-02 2.50e+03 1.17e+00 bond pdb=" C2 RTV B1001 " pdb=" C3 RTV B1001 " ideal model delta sigma weight residual 1.547 1.525 0.022 2.00e-02 2.50e+03 1.17e+00 bond pdb=" C4 RTV B1001 " pdb=" C5 RTV B1001 " ideal model delta sigma weight residual 1.547 1.526 0.021 2.00e-02 2.50e+03 1.12e+00 ... (remaining 5191 not shown) Histogram of bond angle deviations from ideal: 100.83 - 107.46: 173 107.46 - 114.09: 2722 114.09 - 120.72: 2177 120.72 - 127.35: 1958 127.35 - 133.99: 52 Bond angle restraints: 7082 Sorted by residual: angle pdb=" N TYR C 109 " pdb=" CA TYR C 109 " pdb=" C TYR C 109 " ideal model delta sigma weight residual 108.34 105.46 2.88 1.64e+00 3.72e-01 3.09e+00 angle pdb=" N TYR A 109 " pdb=" CA TYR A 109 " pdb=" C TYR A 109 " ideal model delta sigma weight residual 108.34 105.46 2.88 1.64e+00 3.72e-01 3.08e+00 angle pdb=" CA TYR B 369 " pdb=" CB TYR B 369 " pdb=" CG TYR B 369 " ideal model delta sigma weight residual 113.90 116.98 -3.08 1.80e+00 3.09e-01 2.93e+00 angle pdb=" CA TYR D 369 " pdb=" CB TYR D 369 " pdb=" CG TYR D 369 " ideal model delta sigma weight residual 113.90 116.95 -3.05 1.80e+00 3.09e-01 2.87e+00 angle pdb=" N ASP A 119 " pdb=" CA ASP A 119 " pdb=" C ASP A 119 " ideal model delta sigma weight residual 111.36 113.10 -1.74 1.09e+00 8.42e-01 2.54e+00 ... (remaining 7077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.37: 2892 22.37 - 44.73: 96 44.73 - 67.10: 14 67.10 - 89.47: 12 89.47 - 111.84: 14 Dihedral angle restraints: 3028 sinusoidal: 1140 harmonic: 1888 Sorted by residual: dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 96 " pdb=" CB CYS C 96 " ideal model delta sinusoidal sigma weight residual 93.00 57.00 36.00 1 1.00e+01 1.00e-02 1.83e+01 dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 96 " pdb=" CB CYS A 96 " ideal model delta sinusoidal sigma weight residual 93.00 57.02 35.98 1 1.00e+01 1.00e-02 1.83e+01 dihedral pdb=" C2 RTV D1001 " pdb=" C3 RTV D1001 " pdb=" C4 RTV D1001 " pdb=" C5 RTV D1001 " ideal model delta sinusoidal sigma weight residual -57.83 54.01 -111.84 1 3.00e+01 1.11e-03 1.46e+01 ... (remaining 3025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.000: 745 1.000 - 2.000: 0 2.000 - 3.001: 0 3.001 - 4.001: 0 4.001 - 5.001: 2 Chirality restraints: 747 Sorted by residual: chirality pdb=" C2 RTV D1001 " pdb=" C1 RTV D1001 " pdb=" C3 RTV D1001 " pdb=" N2 RTV D1001 " both_signs ideal model delta sigma weight residual False 2.50 -2.50 5.00 2.00e-01 2.50e+01 6.25e+02 chirality pdb=" C2 RTV B1001 " pdb=" C1 RTV B1001 " pdb=" C3 RTV B1001 " pdb=" N2 RTV B1001 " both_signs ideal model delta sigma weight residual False 2.50 -2.50 5.00 2.00e-01 2.50e+01 6.25e+02 chirality pdb=" CA ILE A 51 " pdb=" N ILE A 51 " pdb=" C ILE A 51 " pdb=" CB ILE A 51 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 ... (remaining 744 not shown) Planarity restraints: 927 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 116 " 0.010 2.00e-02 2.50e+03 7.11e-03 1.27e+00 pdb=" CG TRP C 116 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP C 116 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP C 116 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 116 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 116 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 116 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 116 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 116 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 116 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 116 " -0.010 2.00e-02 2.50e+03 6.98e-03 1.22e+00 pdb=" CG TRP A 116 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP A 116 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 116 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 116 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 116 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 116 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 116 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 116 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 116 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 109 " -0.006 2.00e-02 2.50e+03 6.69e-03 8.94e-01 pdb=" CG TYR C 109 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR C 109 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR C 109 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 109 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 109 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 109 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 109 " 0.001 2.00e-02 2.50e+03 ... (remaining 924 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 1066 2.78 - 3.31: 4472 3.31 - 3.84: 8618 3.84 - 4.37: 10549 4.37 - 4.90: 17846 Nonbonded interactions: 42551 Sorted by model distance: nonbonded pdb=" ND2 ASN B 343 " pdb=" O7 RTV B1001 " model vdw 2.255 2.520 nonbonded pdb=" N GLY C 15 " pdb=" O LEU C 86 " model vdw 2.557 2.520 nonbonded pdb=" N GLY A 15 " pdb=" O LEU A 86 " model vdw 2.557 2.520 nonbonded pdb=" N GLN C 13 " pdb=" OE1 GLN C 13 " model vdw 2.571 2.520 nonbonded pdb=" N GLN A 13 " pdb=" OE1 GLN A 13 " model vdw 2.572 2.520 ... (remaining 42546 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 2 through 133) selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 333 through 381 or (resid 382 and (name N or name CA or na \ me C or name O or name CB )) or resid 383 through 527 or resid 1001)) selection = chain 'D' } 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: 0.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.550 Find NCS groups from input model: 0.290 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:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 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 : 0.003 0.028 5196 Z= 0.184 Angle : 0.549 4.419 7082 Z= 0.304 Chirality : 0.263 5.001 747 Planarity : 0.004 0.023 927 Dihedral : 15.471 111.836 1814 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.34 (0.31), residues: 648 helix: -0.59 (0.84), residues: 36 sheet: 2.74 (0.37), residues: 164 loop : 0.35 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 116 HIS 0.000 0.000 HIS B 519 PHE 0.012 0.001 PHE B 347 TYR 0.016 0.001 TYR C 109 ARG 0.002 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 420 ASP cc_start: 0.8321 (m-30) cc_final: 0.8049 (m-30) REVERT: B 483 VAL cc_start: 0.8283 (t) cc_final: 0.8058 (m) REVERT: D 493 GLN cc_start: 0.8064 (tp40) cc_final: 0.7738 (tp40) REVERT: A 73 ASP cc_start: 0.8075 (t0) cc_final: 0.7862 (t0) REVERT: C 32 TYR cc_start: 0.9068 (m-80) cc_final: 0.8781 (m-80) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.9363 time to fit residues: 159.8205 Evaluate side-chains 116 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 20.0000 chunk 48 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 19 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 chunk 58 optimal weight: 20.0000 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN A 74 ASN C 3 GLN C 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 5196 Z= 0.366 Angle : 0.599 6.313 7082 Z= 0.319 Chirality : 0.047 0.163 747 Planarity : 0.004 0.034 927 Dihedral : 6.717 46.210 770 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 4.41 % Allowed : 13.60 % Favored : 81.99 % 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: 0.60 (0.32), residues: 648 helix: -1.52 (0.86), residues: 30 sheet: 1.31 (0.37), residues: 201 loop : 0.15 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 116 HIS 0.001 0.001 HIS D 519 PHE 0.016 0.002 PHE B 347 TYR 0.021 0.002 TYR B 495 ARG 0.004 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 122 time to evaluate : 0.619 Fit side-chains REVERT: B 420 ASP cc_start: 0.8280 (m-30) cc_final: 0.8000 (m-30) REVERT: B 465 GLU cc_start: 0.8893 (tt0) cc_final: 0.8485 (tt0) REVERT: D 420 ASP cc_start: 0.8509 (m-30) cc_final: 0.8121 (m-30) REVERT: D 493 GLN cc_start: 0.7981 (tp40) cc_final: 0.7716 (tp40) REVERT: D 498 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8284 (mp10) REVERT: A 6 GLU cc_start: 0.7899 (mp0) cc_final: 0.7592 (mp0) REVERT: A 89 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7889 (mp0) REVERT: C 32 TYR cc_start: 0.9174 (m-80) cc_final: 0.8841 (m-80) REVERT: C 95 TYR cc_start: 0.9190 (m-80) cc_final: 0.8772 (m-80) outliers start: 23 outliers final: 10 residues processed: 129 average time/residue: 0.7916 time to fit residues: 108.2609 Evaluate side-chains 126 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 114 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 79 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 40.0000 chunk 18 optimal weight: 20.0000 chunk 48 optimal weight: 20.0000 chunk 39 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 20.0000 chunk 57 optimal weight: 0.8980 chunk 19 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 overall best weight: 6.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN B 501 ASN D 487 ASN A 74 ASN A 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5196 Z= 0.277 Angle : 0.535 8.514 7082 Z= 0.282 Chirality : 0.044 0.142 747 Planarity : 0.004 0.035 927 Dihedral : 5.753 35.676 770 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 5.36 % Allowed : 17.05 % Favored : 77.59 % 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: 0.32 (0.31), residues: 648 helix: -1.66 (0.96), residues: 24 sheet: 1.37 (0.37), residues: 187 loop : -0.18 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 116 HIS 0.001 0.000 HIS B 519 PHE 0.010 0.001 PHE B 490 TYR 0.015 0.001 TYR B 495 ARG 0.002 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 117 time to evaluate : 0.594 Fit side-chains revert: symmetry clash REVERT: B 420 ASP cc_start: 0.8358 (m-30) cc_final: 0.8110 (m-30) REVERT: B 465 GLU cc_start: 0.8909 (tt0) cc_final: 0.8391 (tt0) REVERT: B 493 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.7248 (tm-30) REVERT: D 420 ASP cc_start: 0.8504 (m-30) cc_final: 0.8178 (m-30) REVERT: D 493 GLN cc_start: 0.8024 (tp40) cc_final: 0.7761 (tp40) REVERT: D 498 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8218 (mp10) REVERT: A 6 GLU cc_start: 0.7974 (mp0) cc_final: 0.7591 (mp0) REVERT: A 46 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7468 (pt0) REVERT: A 89 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7802 (mp0) REVERT: A 103 SER cc_start: 0.8621 (m) cc_final: 0.8420 (p) REVERT: C 32 TYR cc_start: 0.9190 (m-80) cc_final: 0.8921 (m-80) REVERT: C 95 TYR cc_start: 0.9171 (m-80) cc_final: 0.8864 (m-80) outliers start: 28 outliers final: 13 residues processed: 128 average time/residue: 0.8281 time to fit residues: 112.3856 Evaluate side-chains 128 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 111 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain D residue 405 ASP Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 79 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 0.4980 chunk 43 optimal weight: 0.4980 chunk 30 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 chunk 58 optimal weight: 3.9990 chunk 61 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 51 optimal weight: 20.0000 overall best weight: 4.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN D 487 ASN A 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 5196 Z= 0.240 Angle : 0.519 9.544 7082 Z= 0.271 Chirality : 0.043 0.171 747 Planarity : 0.004 0.036 927 Dihedral : 5.365 34.225 770 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 5.75 % Allowed : 16.86 % Favored : 77.39 % 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: 0.20 (0.30), residues: 648 helix: -1.66 (0.96), residues: 24 sheet: 1.34 (0.37), residues: 177 loop : -0.25 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 116 HIS 0.001 0.000 HIS D 519 PHE 0.007 0.001 PHE A 68 TYR 0.011 0.001 TYR B 495 ARG 0.002 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 117 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: B 420 ASP cc_start: 0.8354 (m-30) cc_final: 0.8112 (m-30) REVERT: B 493 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.7200 (tm-30) REVERT: D 420 ASP cc_start: 0.8533 (m-30) cc_final: 0.8189 (m-30) REVERT: D 467 ASP cc_start: 0.8130 (t0) cc_final: 0.7879 (t0) REVERT: D 493 GLN cc_start: 0.8028 (tp40) cc_final: 0.7792 (tp40) REVERT: D 498 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8197 (mp10) REVERT: A 6 GLU cc_start: 0.7996 (mp0) cc_final: 0.7569 (mp0) REVERT: A 46 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7524 (pt0) REVERT: C 32 TYR cc_start: 0.9173 (m-80) cc_final: 0.8888 (m-80) REVERT: C 95 TYR cc_start: 0.9166 (m-80) cc_final: 0.8805 (m-80) outliers start: 30 outliers final: 19 residues processed: 132 average time/residue: 0.7030 time to fit residues: 99.1609 Evaluate side-chains 132 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 110 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 129 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN C 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 5196 Z= 0.249 Angle : 0.561 10.969 7082 Z= 0.291 Chirality : 0.044 0.215 747 Planarity : 0.004 0.047 927 Dihedral : 5.460 34.217 770 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.85 % Favored : 97.99 % Rotamer: Outliers : 6.90 % Allowed : 17.43 % Favored : 75.67 % 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: 0.04 (0.30), residues: 648 helix: -2.19 (1.09), residues: 18 sheet: 1.16 (0.36), residues: 177 loop : -0.34 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 116 HIS 0.001 0.000 HIS D 519 PHE 0.013 0.001 PHE B 392 TYR 0.012 0.001 TYR B 495 ARG 0.001 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 112 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: B 420 ASP cc_start: 0.8347 (m-30) cc_final: 0.7906 (m-30) REVERT: B 493 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.7204 (tm-30) REVERT: D 420 ASP cc_start: 0.8512 (m-30) cc_final: 0.8166 (m-30) REVERT: D 467 ASP cc_start: 0.8143 (t0) cc_final: 0.7874 (t0) REVERT: D 493 GLN cc_start: 0.8020 (tp40) cc_final: 0.7802 (tp40) REVERT: D 498 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8194 (mp10) REVERT: A 6 GLU cc_start: 0.8080 (mp0) cc_final: 0.7596 (mp0) REVERT: A 46 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7536 (pt0) REVERT: C 32 TYR cc_start: 0.9184 (m-80) cc_final: 0.8929 (m-80) REVERT: C 95 TYR cc_start: 0.9168 (m-80) cc_final: 0.8848 (m-80) outliers start: 36 outliers final: 22 residues processed: 128 average time/residue: 0.6789 time to fit residues: 93.0409 Evaluate side-chains 136 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 111 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 129 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 61 optimal weight: 20.0000 chunk 51 optimal weight: 7.9990 chunk 28 optimal weight: 20.0000 chunk 5 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 6 optimal weight: 20.0000 chunk 35 optimal weight: 7.9990 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN C 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5196 Z= 0.254 Angle : 0.557 11.593 7082 Z= 0.288 Chirality : 0.044 0.181 747 Planarity : 0.004 0.036 927 Dihedral : 5.399 34.523 770 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 6.51 % Allowed : 18.77 % Favored : 74.71 % 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: -0.10 (0.30), residues: 648 helix: -2.30 (1.06), residues: 18 sheet: 1.02 (0.36), residues: 177 loop : -0.42 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 436 HIS 0.001 0.000 HIS B 519 PHE 0.014 0.001 PHE B 392 TYR 0.012 0.001 TYR B 495 ARG 0.002 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 111 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 420 ASP cc_start: 0.8334 (m-30) cc_final: 0.7899 (m-30) REVERT: B 493 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.7214 (tm-30) REVERT: D 420 ASP cc_start: 0.8524 (m-30) cc_final: 0.8191 (m-30) REVERT: D 467 ASP cc_start: 0.8130 (t0) cc_final: 0.7894 (t0) REVERT: D 493 GLN cc_start: 0.8050 (tp40) cc_final: 0.7838 (tp40) REVERT: D 498 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8190 (mp10) REVERT: A 6 GLU cc_start: 0.8121 (mp0) cc_final: 0.7606 (mp0) REVERT: A 46 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7539 (pt0) REVERT: C 32 TYR cc_start: 0.9196 (m-80) cc_final: 0.8923 (m-80) REVERT: C 82 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.7346 (tm-30) outliers start: 34 outliers final: 20 residues processed: 127 average time/residue: 0.7564 time to fit residues: 102.4482 Evaluate side-chains 133 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 109 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain D residue 405 ASP Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 129 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 34 optimal weight: 0.4980 chunk 61 optimal weight: 20.0000 chunk 38 optimal weight: 30.0000 chunk 37 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5196 Z= 0.200 Angle : 0.545 12.056 7082 Z= 0.280 Chirality : 0.043 0.167 747 Planarity : 0.004 0.033 927 Dihedral : 5.169 33.293 770 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 6.32 % Allowed : 19.73 % Favored : 73.95 % 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: -0.13 (0.30), residues: 648 helix: -2.28 (1.06), residues: 18 sheet: 0.96 (0.36), residues: 177 loop : -0.43 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 436 HIS 0.000 0.000 HIS D 519 PHE 0.013 0.001 PHE B 392 TYR 0.009 0.001 TYR B 495 ARG 0.001 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 109 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 420 ASP cc_start: 0.8306 (m-30) cc_final: 0.8105 (m-30) REVERT: B 493 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.7202 (tm-30) REVERT: D 420 ASP cc_start: 0.8485 (m-30) cc_final: 0.8141 (m-30) REVERT: D 467 ASP cc_start: 0.8097 (t0) cc_final: 0.7888 (t0) REVERT: D 493 GLN cc_start: 0.8047 (tp40) cc_final: 0.7838 (tp40) REVERT: D 498 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8115 (mp10) REVERT: D 517 LEU cc_start: 0.8092 (tp) cc_final: 0.7865 (tt) REVERT: A 6 GLU cc_start: 0.8083 (mp0) cc_final: 0.7673 (mp0) REVERT: A 46 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7497 (pt0) REVERT: A 89 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7955 (mp0) REVERT: C 32 TYR cc_start: 0.9181 (m-80) cc_final: 0.8943 (m-80) REVERT: C 82 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.7313 (tm-30) outliers start: 33 outliers final: 21 residues processed: 126 average time/residue: 0.7519 time to fit residues: 101.2009 Evaluate side-chains 134 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 108 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain D residue 405 ASP Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 129 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 6.9990 chunk 11 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5196 Z= 0.270 Angle : 0.560 11.165 7082 Z= 0.288 Chirality : 0.044 0.175 747 Planarity : 0.004 0.034 927 Dihedral : 5.404 36.149 770 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 6.13 % Allowed : 20.31 % Favored : 73.56 % 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: -0.20 (0.30), residues: 648 helix: -2.43 (1.03), residues: 18 sheet: 0.87 (0.36), residues: 177 loop : -0.45 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 436 HIS 0.000 0.000 HIS B 519 PHE 0.011 0.001 PHE B 392 TYR 0.013 0.001 TYR B 495 ARG 0.002 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 115 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 420 ASP cc_start: 0.8333 (m-30) cc_final: 0.8123 (m-30) REVERT: B 493 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.7236 (tm-30) REVERT: B 498 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8385 (mp10) REVERT: D 420 ASP cc_start: 0.8536 (m-30) cc_final: 0.8253 (m-30) REVERT: D 467 ASP cc_start: 0.8115 (t0) cc_final: 0.7874 (t0) REVERT: D 493 GLN cc_start: 0.8031 (tp40) cc_final: 0.7827 (tp40) REVERT: D 498 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8177 (mp10) REVERT: D 517 LEU cc_start: 0.8148 (tp) cc_final: 0.7931 (tt) REVERT: A 6 GLU cc_start: 0.8102 (mp0) cc_final: 0.7677 (mp0) REVERT: A 45 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7611 (mtt180) REVERT: A 46 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7559 (pt0) REVERT: C 32 TYR cc_start: 0.9216 (m-80) cc_final: 0.8986 (m-80) REVERT: C 82 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.7282 (tm-30) outliers start: 32 outliers final: 22 residues processed: 131 average time/residue: 0.7624 time to fit residues: 106.2191 Evaluate side-chains 140 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 112 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain D residue 405 ASP Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 129 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 17 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 60 optimal weight: 30.0000 chunk 28 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 5196 Z= 0.276 Angle : 0.574 10.703 7082 Z= 0.297 Chirality : 0.044 0.180 747 Planarity : 0.004 0.035 927 Dihedral : 5.453 36.148 770 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.78 % Favored : 97.07 % Rotamer: Outliers : 5.56 % Allowed : 21.07 % Favored : 73.37 % 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: -0.28 (0.30), residues: 648 helix: -2.50 (1.02), residues: 18 sheet: 0.81 (0.36), residues: 177 loop : -0.50 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 436 HIS 0.000 0.000 HIS D 519 PHE 0.011 0.001 PHE B 392 TYR 0.013 0.001 TYR B 495 ARG 0.001 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 110 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 420 ASP cc_start: 0.8334 (m-30) cc_final: 0.8124 (m-30) REVERT: B 493 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.7231 (tm-30) REVERT: B 498 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8380 (mp10) REVERT: D 420 ASP cc_start: 0.8503 (m-30) cc_final: 0.8199 (m-30) REVERT: D 467 ASP cc_start: 0.8130 (t0) cc_final: 0.7884 (t0) REVERT: D 493 GLN cc_start: 0.8020 (tp40) cc_final: 0.7817 (tp40) REVERT: D 498 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8159 (mp10) REVERT: D 517 LEU cc_start: 0.8151 (tp) cc_final: 0.7934 (tt) REVERT: A 6 GLU cc_start: 0.8109 (mp0) cc_final: 0.7573 (mp0) REVERT: A 46 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7579 (pt0) REVERT: C 32 TYR cc_start: 0.9220 (m-80) cc_final: 0.8973 (m-80) REVERT: C 82 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.7370 (tm-30) outliers start: 29 outliers final: 21 residues processed: 122 average time/residue: 0.7661 time to fit residues: 99.4024 Evaluate side-chains 135 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 109 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain D residue 405 ASP Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 50 optimal weight: 30.0000 chunk 5 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 40 optimal weight: 20.0000 chunk 54 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5196 Z= 0.200 Angle : 0.534 10.382 7082 Z= 0.274 Chirality : 0.043 0.160 747 Planarity : 0.003 0.035 927 Dihedral : 5.170 32.483 770 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.16 % Favored : 97.69 % Rotamer: Outliers : 5.17 % Allowed : 21.46 % Favored : 73.37 % 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: -0.27 (0.30), residues: 648 helix: -2.47 (1.03), residues: 18 sheet: 0.82 (0.36), residues: 177 loop : -0.49 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 436 HIS 0.000 0.000 HIS D 519 PHE 0.011 0.001 PHE B 392 TYR 0.010 0.001 TYR B 495 ARG 0.001 0.000 ARG C 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 109 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 493 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.7207 (tm-30) REVERT: B 498 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8388 (mp10) REVERT: B 517 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8560 (tt) REVERT: D 420 ASP cc_start: 0.8525 (m-30) cc_final: 0.8178 (m-30) REVERT: D 467 ASP cc_start: 0.8076 (t0) cc_final: 0.7867 (t0) REVERT: D 493 GLN cc_start: 0.8039 (tp40) cc_final: 0.7835 (tp40) REVERT: D 498 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8146 (mp10) REVERT: D 517 LEU cc_start: 0.8117 (tp) cc_final: 0.7908 (tt) REVERT: A 6 GLU cc_start: 0.8085 (mp0) cc_final: 0.7660 (mp0) REVERT: A 45 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7618 (mtt180) REVERT: A 46 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7511 (pt0) REVERT: C 32 TYR cc_start: 0.9192 (m-80) cc_final: 0.8977 (m-80) outliers start: 27 outliers final: 20 residues processed: 123 average time/residue: 0.7822 time to fit residues: 102.2373 Evaluate side-chains 134 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 108 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain D residue 405 ASP Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 9.9990 chunk 14 optimal weight: 0.2980 chunk 50 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 52 optimal weight: 20.0000 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 overall best weight: 5.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.097614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.082476 restraints weight = 8659.647| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.79 r_work: 0.3023 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 5196 Z= 0.243 Angle : 0.557 10.212 7082 Z= 0.288 Chirality : 0.044 0.165 747 Planarity : 0.004 0.035 927 Dihedral : 5.284 34.341 770 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.78 % Favored : 97.07 % Rotamer: Outliers : 5.75 % Allowed : 21.07 % Favored : 73.18 % 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: -0.29 (0.30), residues: 648 helix: -2.50 (1.02), residues: 18 sheet: 0.74 (0.36), residues: 177 loop : -0.49 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 436 HIS 0.000 0.000 HIS D 519 PHE 0.008 0.001 PHE B 490 TYR 0.012 0.001 TYR B 495 ARG 0.001 0.000 ARG C 19 =============================================================================== Job complete usr+sys time: 2198.14 seconds wall clock time: 39 minutes 37.96 seconds (2377.96 seconds total)