Starting phenix.real_space_refine on Thu Nov 14 07:24:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zlo_60231/11_2024/8zlo_60231.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zlo_60231/11_2024/8zlo_60231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zlo_60231/11_2024/8zlo_60231.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zlo_60231/11_2024/8zlo_60231.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zlo_60231/11_2024/8zlo_60231.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zlo_60231/11_2024/8zlo_60231.cif" } resolution = 3.1 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= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Br 10 7.06 5 S 10 5.16 5 C 3030 2.51 5 N 836 2.21 5 O 920 1.98 5 F 10 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 4816 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "B" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "C" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "D" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "E" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "F" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "G" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "H" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "I" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "J" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "O" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "T" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'1KI': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'1KI': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'1KI': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'1KI': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'1KI': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'1KI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.24, per 1000 atoms: 0.67 Number of scatterers: 4816 At special positions: 0 Unit cell: (78.85, 96.28, 49.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Br 10 34.99 S 10 16.00 F 10 9.00 O 920 8.00 N 836 7.00 C 3030 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 583.1 milliseconds 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1128 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 48 removed outlier: 6.723A pdb=" N GLY A 47 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY E 47 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 63 through 64 removed outlier: 6.423A pdb=" N VAL A 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL E 63 " --> pdb=" O THR I 64 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N THR E 64 " --> pdb=" O ASN J 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 69 through 71 removed outlier: 6.511A pdb=" N VAL A 70 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL E 70 " --> pdb=" O VAL I 71 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 75 through 78 removed outlier: 6.360A pdb=" N ALA A 76 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ALA E 76 " --> pdb=" O VAL I 77 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 90 through 93 removed outlier: 8.872A pdb=" N ALA A 90 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N GLY B 93 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N THR A 92 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA A 91 " --> pdb=" O ALA I 90 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR I 92 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N ALA E 90 " --> pdb=" O ALA I 91 " (cutoff:3.500A) removed outlier: 9.083A pdb=" N GLY I 93 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N THR E 92 " --> pdb=" O GLY I 93 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ALA E 91 " --> pdb=" O ALA J 90 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR J 92 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ALA J 91 " --> pdb=" O ALA T 90 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR T 92 " --> pdb=" O ALA J 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 46 through 48 removed outlier: 6.723A pdb=" N GLY C 47 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLY F 47 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 63 through 64 removed outlier: 6.423A pdb=" N VAL C 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL F 63 " --> pdb=" O THR G 64 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N THR F 64 " --> pdb=" O ASN H 65 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 69 through 71 removed outlier: 6.512A pdb=" N VAL C 70 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL F 70 " --> pdb=" O VAL G 71 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 75 through 78 removed outlier: 6.361A pdb=" N ALA C 76 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA F 76 " --> pdb=" O VAL G 77 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 90 through 93 removed outlier: 8.872A pdb=" N ALA C 90 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N GLY D 93 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N THR C 92 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA C 91 " --> pdb=" O ALA G 90 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR G 92 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N ALA F 90 " --> pdb=" O ALA G 91 " (cutoff:3.500A) removed outlier: 9.083A pdb=" N GLY G 93 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N THR F 92 " --> pdb=" O GLY G 93 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ALA F 91 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR H 92 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ALA H 91 " --> pdb=" O ALA O 90 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR O 92 " --> pdb=" O ALA H 91 " (cutoff:3.500A) 60 hydrogen bonds defined for protein. 180 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: 1.08 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 1582 1.35 - 1.50: 1415 1.50 - 1.65: 1821 1.65 - 1.79: 20 1.79 - 1.94: 10 Bond restraints: 4848 Sorted by residual: bond pdb=" C13 1KI I 101 " pdb=" C14 1KI I 101 " ideal model delta sigma weight residual 1.409 1.297 0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" C13 1KI G 101 " pdb=" C14 1KI G 101 " ideal model delta sigma weight residual 1.409 1.297 0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" C12 1KI G 101 " pdb=" C13 1KI G 101 " ideal model delta sigma weight residual 1.390 1.466 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C12 1KI I 101 " pdb=" C13 1KI I 101 " ideal model delta sigma weight residual 1.390 1.465 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C13 1KI G 103 " pdb=" C14 1KI G 103 " ideal model delta sigma weight residual 1.409 1.340 0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 4843 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 5855 2.35 - 4.71: 564 4.71 - 7.06: 95 7.06 - 9.42: 16 9.42 - 11.77: 12 Bond angle restraints: 6542 Sorted by residual: angle pdb=" C03 1KI I 101 " pdb=" N04 1KI I 101 " pdb=" C05 1KI I 101 " ideal model delta sigma weight residual 115.28 127.05 -11.77 3.00e+00 1.11e-01 1.54e+01 angle pdb=" C03 1KI G 101 " pdb=" N04 1KI G 101 " pdb=" C05 1KI G 101 " ideal model delta sigma weight residual 115.28 127.01 -11.73 3.00e+00 1.11e-01 1.53e+01 angle pdb=" N ILE E 88 " pdb=" CA ILE E 88 " pdb=" C ILE E 88 " ideal model delta sigma weight residual 108.12 103.39 4.73 1.34e+00 5.57e-01 1.24e+01 angle pdb=" N ILE F 88 " pdb=" CA ILE F 88 " pdb=" C ILE F 88 " ideal model delta sigma weight residual 108.12 103.41 4.71 1.34e+00 5.57e-01 1.24e+01 angle pdb=" N ILE C 88 " pdb=" CA ILE C 88 " pdb=" C ILE C 88 " ideal model delta sigma weight residual 108.12 103.42 4.70 1.34e+00 5.57e-01 1.23e+01 ... (remaining 6537 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 2504 17.68 - 35.37: 185 35.37 - 53.05: 66 53.05 - 70.74: 15 70.74 - 88.42: 18 Dihedral angle restraints: 2788 sinusoidal: 1012 harmonic: 1776 Sorted by residual: dihedral pdb=" CA GLY G 67 " pdb=" C GLY G 67 " pdb=" N GLY G 68 " pdb=" CA GLY G 68 " ideal model delta harmonic sigma weight residual 0.00 25.06 -25.06 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA GLY O 67 " pdb=" C GLY O 67 " pdb=" N GLY O 68 " pdb=" CA GLY O 68 " ideal model delta harmonic sigma weight residual 0.00 25.05 -25.05 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA GLY D 67 " pdb=" C GLY D 67 " pdb=" N GLY D 68 " pdb=" CA GLY D 68 " ideal model delta harmonic sigma weight residual 0.00 25.05 -25.05 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 2785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 436 0.052 - 0.104: 202 0.104 - 0.157: 118 0.157 - 0.209: 24 0.209 - 0.261: 24 Chirality restraints: 804 Sorted by residual: chirality pdb=" CA ILE J 88 " pdb=" N ILE J 88 " pdb=" C ILE J 88 " pdb=" CB ILE J 88 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA ILE H 88 " pdb=" N ILE H 88 " pdb=" C ILE H 88 " pdb=" CB ILE H 88 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA ILE A 88 " pdb=" N ILE A 88 " pdb=" C ILE A 88 " pdb=" CB ILE A 88 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 801 not shown) Planarity restraints: 808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 52 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.12e+00 pdb=" C VAL D 52 " 0.039 2.00e-02 2.50e+03 pdb=" O VAL D 52 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA D 53 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 52 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.08e+00 pdb=" C VAL B 52 " -0.039 2.00e-02 2.50e+03 pdb=" O VAL B 52 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA B 53 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 52 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.00e+00 pdb=" C VAL E 52 " -0.039 2.00e-02 2.50e+03 pdb=" O VAL E 52 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA E 53 " 0.013 2.00e-02 2.50e+03 ... (remaining 805 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 86 2.63 - 3.20: 3873 3.20 - 3.77: 7134 3.77 - 4.33: 9965 4.33 - 4.90: 19076 Nonbonded interactions: 40134 Sorted by model distance: nonbonded pdb=" O GLY D 51 " pdb=" O24 1KI G 103 " model vdw 2.063 3.040 nonbonded pdb=" O GLY B 51 " pdb=" O24 1KI I 103 " model vdw 2.064 3.040 nonbonded pdb=" O GLY G 51 " pdb=" O24 1KI H 101 " model vdw 2.123 3.040 nonbonded pdb=" O GLY I 51 " pdb=" O24 1KI J 101 " model vdw 2.123 3.040 nonbonded pdb=" O GLY A 51 " pdb=" O24 1KI E 101 " model vdw 2.157 3.040 ... (remaining 40129 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = (chain 'E' and resid 45 through 99) selection = (chain 'F' and resid 45 through 99) selection = (chain 'G' and resid 45 through 99) selection = (chain 'H' and resid 45 through 99) selection = (chain 'I' and resid 45 through 99) selection = (chain 'J' and resid 45 through 99) selection = chain 'O' selection = chain 'T' } 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: 0.940 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: 0.020 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.140 Find NCS groups from input model: 0.220 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5204 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 : 0.015 0.112 4848 Z= 0.979 Angle : 1.517 11.774 6542 Z= 0.797 Chirality : 0.081 0.261 804 Planarity : 0.006 0.023 808 Dihedral : 17.146 88.421 1660 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 28.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 0.00 % Allowed : 15.79 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -4.08 (0.25), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.19), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS G 50 PHE 0.016 0.008 PHE C 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.457 Fit side-chains REVERT: F 83 GLU cc_start: 0.6332 (mt-10) cc_final: 0.5759 (mp0) REVERT: H 83 GLU cc_start: 0.5988 (mt-10) cc_final: 0.5785 (mt-10) REVERT: I 72 THR cc_start: 0.7197 (m) cc_final: 0.6914 (p) REVERT: J 83 GLU cc_start: 0.5695 (mt-10) cc_final: 0.5280 (mp0) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.2106 time to fit residues: 19.9032 Evaluate side-chains 55 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 ASN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 ASN ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 ASN ** O 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5601 moved from start: 0.5525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 4848 Z= 0.414 Angle : 1.091 13.937 6542 Z= 0.499 Chirality : 0.056 0.159 804 Planarity : 0.003 0.015 808 Dihedral : 14.141 92.050 748 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 6.58 % Allowed : 12.72 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.91 (0.24), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.18), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS G 50 PHE 0.019 0.004 PHE H 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 53 time to evaluate : 0.459 Fit side-chains REVERT: D 97 LYS cc_start: 0.6964 (mmtt) cc_final: 0.6764 (mttm) outliers start: 30 outliers final: 25 residues processed: 78 average time/residue: 0.1963 time to fit residues: 19.1232 Evaluate side-chains 73 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 48 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 52 VAL Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 15 optimal weight: 0.3980 chunk 54 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 HIS ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5674 moved from start: 0.6245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4848 Z= 0.333 Angle : 0.893 12.416 6542 Z= 0.415 Chirality : 0.054 0.156 804 Planarity : 0.003 0.014 808 Dihedral : 11.224 80.063 748 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 8.33 % Allowed : 8.99 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -4.02 (0.24), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.18), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 50 PHE 0.011 0.002 PHE A 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 58 time to evaluate : 0.483 Fit side-chains REVERT: A 79 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7853 (mt0) REVERT: C 97 LYS cc_start: 0.7152 (mttp) cc_final: 0.6911 (mttp) REVERT: D 79 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7830 (mt0) REVERT: E 79 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7802 (mt0) REVERT: F 79 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7748 (mt0) REVERT: G 79 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7861 (mt0) REVERT: I 79 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7779 (mt0) REVERT: I 97 LYS cc_start: 0.6630 (mttm) cc_final: 0.6328 (mttp) REVERT: J 79 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7696 (mt0) REVERT: T 97 LYS cc_start: 0.7664 (mttm) cc_final: 0.7457 (mttm) REVERT: T 98 ASP cc_start: 0.6214 (m-30) cc_final: 0.5808 (m-30) outliers start: 38 outliers final: 27 residues processed: 87 average time/residue: 0.2139 time to fit residues: 22.8721 Evaluate side-chains 87 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 53 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 52 VAL Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5707 moved from start: 0.7139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 4848 Z= 0.406 Angle : 0.902 12.636 6542 Z= 0.423 Chirality : 0.055 0.157 804 Planarity : 0.003 0.013 808 Dihedral : 10.481 73.820 748 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 7.89 % Allowed : 8.99 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -4.15 (0.24), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.18), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 50 PHE 0.013 0.003 PHE C 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 63 time to evaluate : 0.490 Fit side-chains REVERT: B 79 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7482 (mt0) REVERT: E 79 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7625 (mt0) REVERT: F 79 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7722 (mt0) REVERT: G 79 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7799 (mt0) REVERT: J 79 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7589 (mt0) outliers start: 36 outliers final: 30 residues processed: 88 average time/residue: 0.1869 time to fit residues: 20.6490 Evaluate side-chains 97 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 62 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 52 VAL Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN H 99 GLN T 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5704 moved from start: 0.7321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 4848 Z= 0.322 Angle : 0.814 12.563 6542 Z= 0.377 Chirality : 0.053 0.153 804 Planarity : 0.002 0.013 808 Dihedral : 9.769 72.342 748 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 7.02 % Allowed : 10.09 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -4.16 (0.24), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.19), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 50 PHE 0.011 0.002 PHE C 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 63 time to evaluate : 0.511 Fit side-chains REVERT: B 79 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7561 (mt0) REVERT: D 79 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7866 (mt0) REVERT: E 79 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7772 (mt0) REVERT: F 79 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7722 (mt0) REVERT: G 79 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7788 (mt0) REVERT: I 79 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7731 (mt0) REVERT: J 79 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7705 (mt0) REVERT: J 99 GLN cc_start: 0.3784 (mt0) cc_final: 0.3580 (mt0) REVERT: O 52 VAL cc_start: 0.7534 (OUTLIER) cc_final: 0.7289 (t) outliers start: 32 outliers final: 24 residues processed: 84 average time/residue: 0.1954 time to fit residues: 20.6453 Evaluate side-chains 95 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 63 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain O residue 52 VAL Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 7.9990 chunk 58 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 99 GLN T 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5736 moved from start: 0.7813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.035 4848 Z= 0.520 Angle : 0.956 13.351 6542 Z= 0.454 Chirality : 0.056 0.163 804 Planarity : 0.003 0.010 808 Dihedral : 11.517 76.147 748 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 7.89 % Allowed : 9.87 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -4.28 (0.25), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.19), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 50 PHE 0.015 0.003 PHE C 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 61 time to evaluate : 0.556 Fit side-chains REVERT: B 79 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7498 (mt0) REVERT: D 79 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7911 (mt0) REVERT: E 79 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7711 (mt0) REVERT: F 79 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7740 (mt0) REVERT: G 79 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7863 (mt0) REVERT: J 79 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7766 (mt0) outliers start: 36 outliers final: 30 residues processed: 86 average time/residue: 0.1842 time to fit residues: 20.4072 Evaluate side-chains 96 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 60 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 52 VAL Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 39 optimal weight: 7.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5709 moved from start: 0.7777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 4848 Z= 0.249 Angle : 0.768 12.888 6542 Z= 0.349 Chirality : 0.052 0.151 804 Planarity : 0.002 0.012 808 Dihedral : 10.318 80.963 748 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 6.36 % Allowed : 11.84 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -4.10 (0.25), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.19), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.009 0.002 PHE C 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 65 time to evaluate : 0.482 Fit side-chains REVERT: B 79 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7574 (mt0) REVERT: C 79 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7774 (mt0) REVERT: D 79 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7915 (mt0) REVERT: E 79 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7769 (mt0) REVERT: F 79 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7687 (mt0) REVERT: G 79 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7847 (mt0) REVERT: I 79 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7772 (mt0) REVERT: J 79 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7719 (mt0) outliers start: 29 outliers final: 21 residues processed: 84 average time/residue: 0.1775 time to fit residues: 18.9731 Evaluate side-chains 93 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 64 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain O residue 52 VAL Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 45 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 55 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 99 GLN T 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5744 moved from start: 0.8065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.035 4848 Z= 0.512 Angle : 0.936 13.486 6542 Z= 0.444 Chirality : 0.056 0.164 804 Planarity : 0.003 0.011 808 Dihedral : 11.405 78.859 748 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 7.46 % Allowed : 11.62 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -4.18 (0.25), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.19), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS T 50 PHE 0.015 0.003 PHE I 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 63 time to evaluate : 0.453 Fit side-chains REVERT: B 79 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7517 (mt0) REVERT: D 79 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7987 (mt0) REVERT: E 79 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7724 (mt0) REVERT: F 79 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7715 (mt0) REVERT: G 79 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7899 (mt0) REVERT: G 99 GLN cc_start: 0.4422 (mt0) cc_final: 0.3952 (mp10) REVERT: J 79 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7753 (mt0) outliers start: 34 outliers final: 27 residues processed: 85 average time/residue: 0.1807 time to fit residues: 19.5439 Evaluate side-chains 95 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 62 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain O residue 52 VAL Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 39 optimal weight: 0.2980 chunk 59 optimal weight: 10.0000 chunk 55 optimal weight: 0.4980 chunk 47 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5679 moved from start: 0.7965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4848 Z= 0.123 Angle : 0.681 12.615 6542 Z= 0.303 Chirality : 0.051 0.147 804 Planarity : 0.002 0.011 808 Dihedral : 9.620 81.684 748 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.17 % Allowed : 14.25 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.84 (0.26), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.20), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 50 PHE 0.005 0.001 PHE C 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.492 Fit side-chains REVERT: B 79 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7676 (mt0) REVERT: D 79 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7766 (mt0) REVERT: G 99 GLN cc_start: 0.4134 (mt0) cc_final: 0.3801 (mp10) outliers start: 19 outliers final: 15 residues processed: 75 average time/residue: 0.1906 time to fit residues: 18.0598 Evaluate side-chains 77 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain O residue 52 VAL Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 37 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 99 GLN T 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5710 moved from start: 0.8034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 4848 Z= 0.304 Angle : 0.782 12.934 6542 Z= 0.362 Chirality : 0.052 0.151 804 Planarity : 0.002 0.009 808 Dihedral : 10.091 78.755 748 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 3.95 % Allowed : 15.35 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.91 (0.26), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.20), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 50 PHE 0.011 0.002 PHE C 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.451 Fit side-chains REVERT: B 79 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7553 (mt0) REVERT: D 79 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7943 (mt0) outliers start: 18 outliers final: 16 residues processed: 75 average time/residue: 0.1764 time to fit residues: 16.9427 Evaluate side-chains 82 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain O residue 52 VAL Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 99 GLN T 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.152420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.102965 restraints weight = 2848.693| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.82 r_work: 0.3466 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.8252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.035 4848 Z= 0.500 Angle : 0.937 13.279 6542 Z= 0.447 Chirality : 0.056 0.161 804 Planarity : 0.003 0.011 808 Dihedral : 11.240 77.591 748 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 4.61 % Allowed : 14.47 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -4.11 (0.26), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.20), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 50 PHE 0.014 0.003 PHE C 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1322.78 seconds wall clock time: 25 minutes 7.71 seconds (1507.71 seconds total)