Starting phenix.real_space_refine on Tue Jan 14 00:45:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zlo_60231/01_2025/8zlo_60231.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zlo_60231/01_2025/8zlo_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/cci-nas-00/data/ceres_data/8zlo_60231/01_2025/8zlo_60231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zlo_60231/01_2025/8zlo_60231.map" model { file = "/net/cci-nas-00/data/ceres_data/8zlo_60231/01_2025/8zlo_60231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zlo_60231/01_2025/8zlo_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-5571/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: 3.37, per 1000 atoms: 0.70 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: 1.21 Conformation dependent library (CDL) restraints added in 508.7 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: 0.67 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: 1.10 Time building geometry restraints manager: 1.38 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' selection = chain 'O' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'J' } 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.910 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.990 ------------------------------------------------------------------------------- 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 : 0.477 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: 0.2220 time to fit residues: 21.0068 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 : 0.452 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.170799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.120253 restraints weight = 2746.750| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 1.85 r_work: 0.3671 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 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 : 0.483 Fit side-chains REVERT: H 97 LYS cc_start: 0.8241 (mttt) cc_final: 0.7984 (mttm) outliers start: 30 outliers final: 25 residues processed: 78 average time/residue: 0.1895 time to fit residues: 18.4596 Evaluate side-chains 72 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 47 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 52 optimal weight: 0.1980 chunk 23 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS D 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.161680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.110358 restraints weight = 2660.072| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 1.77 r_work: 0.3564 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.6411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 4848 Z= 0.382 Angle : 0.931 12.442 6542 Z= 0.436 Chirality : 0.055 0.156 804 Planarity : 0.003 0.015 808 Dihedral : 11.556 82.736 748 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 8.77 % Allowed : 8.11 % 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: -4.06 (0.24), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.09 (0.18), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS G 50 PHE 0.013 0.003 PHE D 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 98 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 58 time to evaluate : 0.382 Fit side-chains REVERT: F 79 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8631 (mt0) REVERT: G 97 LYS cc_start: 0.9036 (mttm) cc_final: 0.8810 (mttp) REVERT: H 97 LYS cc_start: 0.8643 (mttt) cc_final: 0.8430 (mttm) REVERT: I 97 LYS cc_start: 0.9021 (mttm) cc_final: 0.8557 (mttp) REVERT: J 79 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8521 (mt0) REVERT: T 98 ASP cc_start: 0.7729 (m-30) cc_final: 0.7383 (m-30) outliers start: 40 outliers final: 28 residues processed: 88 average time/residue: 0.1926 time to fit residues: 20.8858 Evaluate side-chains 80 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 50 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 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 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 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 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 39 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 50 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 GLN O 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.156560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.105288 restraints weight = 2757.672| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.81 r_work: 0.3463 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.7428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.041 4848 Z= 0.531 Angle : 0.998 12.881 6542 Z= 0.475 Chirality : 0.057 0.162 804 Planarity : 0.003 0.012 808 Dihedral : 11.602 78.643 748 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 7.46 % Allowed : 9.87 % 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: -4.25 (0.24), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.19), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS G 50 PHE 0.017 0.004 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 92 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 58 time to evaluate : 0.468 Fit side-chains REVERT: B 79 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8622 (mt0) REVERT: F 79 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8695 (mt0) REVERT: H 97 LYS cc_start: 0.8862 (mttt) cc_final: 0.8647 (mttm) REVERT: J 79 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8603 (mt0) outliers start: 34 outliers final: 29 residues processed: 82 average time/residue: 0.1961 time to fit residues: 20.2076 Evaluate side-chains 91 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 59 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 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 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 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 31 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 16 optimal weight: 0.0980 chunk 18 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 99 GLN H 99 GLN T 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.162359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.112888 restraints weight = 2713.660| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 1.74 r_work: 0.3562 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.7415 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= 0.254 Angle : 0.783 12.617 6542 Z= 0.356 Chirality : 0.052 0.149 804 Planarity : 0.002 0.013 808 Dihedral : 10.186 73.288 748 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 5.92 % Allowed : 12.28 % 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: -4.13 (0.25), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.19), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.010 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 93 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.502 Fit side-chains REVERT: C 79 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8702 (mt0) REVERT: F 79 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8587 (mt0) REVERT: F 98 ASP cc_start: 0.8206 (m-30) cc_final: 0.7951 (m-30) REVERT: I 79 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8726 (mt0) outliers start: 27 outliers final: 22 residues processed: 85 average time/residue: 0.1785 time to fit residues: 19.1679 Evaluate side-chains 88 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 63 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 79 GLN 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 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 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 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: 10.0000 chunk 34 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 55 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 overall best weight: 3.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 99 GLN J 79 GLN T 79 GLN T 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.159504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.109310 restraints weight = 2741.509| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.77 r_work: 0.3491 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.7707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 4848 Z= 0.370 Angle : 0.846 12.938 6542 Z= 0.393 Chirality : 0.053 0.153 804 Planarity : 0.002 0.011 808 Dihedral : 10.693 75.063 748 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 5.92 % Allowed : 11.62 % Favored : 82.46 % 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: -4.09 (0.26), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.20), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 50 PHE 0.012 0.002 PHE I 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 89 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 62 time to evaluate : 0.586 Fit side-chains REVERT: F 79 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8568 (mt0) REVERT: F 97 LYS cc_start: 0.8928 (mttm) cc_final: 0.8707 (mttp) REVERT: H 97 LYS cc_start: 0.8824 (mttm) cc_final: 0.8623 (mttm) REVERT: O 99 GLN cc_start: 0.5534 (mt0) cc_final: 0.5322 (tm-30) outliers start: 27 outliers final: 26 residues processed: 78 average time/residue: 0.1822 time to fit residues: 18.1478 Evaluate side-chains 88 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 61 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 79 GLN 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 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 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 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 8 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 7 optimal weight: 0.1980 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.161651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.112511 restraints weight = 2701.006| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 1.73 r_work: 0.3579 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.7742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4848 Z= 0.214 Angle : 0.732 12.481 6542 Z= 0.330 Chirality : 0.051 0.148 804 Planarity : 0.002 0.011 808 Dihedral : 9.862 77.264 748 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 5.04 % Allowed : 13.16 % 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: -3.92 (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 0.002 0.001 HIS D 50 PHE 0.008 0.002 PHE I 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 88 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 0.491 Fit side-chains REVERT: F 79 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8595 (mt0) REVERT: I 79 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8708 (mt0) outliers start: 23 outliers final: 20 residues processed: 78 average time/residue: 0.1878 time to fit residues: 18.6227 Evaluate side-chains 87 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 52 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 F residue 79 GLN 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 40 optimal weight: 10.0000 chunk 16 optimal weight: 0.1980 chunk 44 optimal weight: 20.0000 chunk 8 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 overall best weight: 5.8388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.156148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.105960 restraints weight = 2774.040| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.75 r_work: 0.3444 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.8132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.036 4848 Z= 0.548 Angle : 0.964 13.597 6542 Z= 0.459 Chirality : 0.057 0.166 804 Planarity : 0.003 0.010 808 Dihedral : 11.387 77.599 748 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 5.70 % Allowed : 12.72 % 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: -4.12 (0.26), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.20), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 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 90 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 0.529 Fit side-chains REVERT: F 79 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8645 (mt0) REVERT: G 99 GLN cc_start: 0.6379 (mt0) cc_final: 0.5839 (mp10) outliers start: 26 outliers final: 24 residues processed: 79 average time/residue: 0.1766 time to fit residues: 17.8842 Evaluate side-chains 88 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 63 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 52 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 F residue 79 GLN 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 H residue 72 THR 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 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 30 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 0.4980 chunk 51 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.161163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.112546 restraints weight = 2885.809| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 1.80 r_work: 0.3640 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.8033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4848 Z= 0.129 Angle : 0.700 12.675 6542 Z= 0.310 Chirality : 0.051 0.144 804 Planarity : 0.002 0.011 808 Dihedral : 9.732 81.468 748 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.73 % Allowed : 14.91 % Favored : 81.36 % 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: -3.79 (0.27), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.20), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 50 PHE 0.006 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 81 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.519 Fit side-chains REVERT: G 99 GLN cc_start: 0.6162 (mt0) cc_final: 0.5707 (mp10) outliers start: 17 outliers final: 16 residues processed: 72 average time/residue: 0.1906 time to fit residues: 17.4642 Evaluate side-chains 78 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 52 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 52 VAL 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 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 33 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 44 optimal weight: 20.0000 chunk 36 optimal weight: 7.9990 chunk 15 optimal weight: 0.1980 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 99 GLN I 99 GLN T 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.155051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.104813 restraints weight = 2835.029| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 1.81 r_work: 0.3499 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.8133 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= 0.359 Angle : 0.826 13.055 6542 Z= 0.385 Chirality : 0.053 0.153 804 Planarity : 0.002 0.009 808 Dihedral : 10.300 77.271 748 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 3.95 % Allowed : 13.38 % 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: -3.91 (0.26), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.20), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS T 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 82 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.453 Fit side-chains REVERT: G 99 GLN cc_start: 0.6338 (mt0) cc_final: 0.5678 (mp10) outliers start: 18 outliers final: 18 residues processed: 73 average time/residue: 0.1873 time to fit residues: 17.6714 Evaluate side-chains 81 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 52 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 52 VAL 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 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 49 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 47 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 1 optimal weight: 0.4980 chunk 56 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 overall best weight: 4.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 99 GLN ** T 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.153900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.103363 restraints weight = 2907.751| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.85 r_work: 0.3486 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.8273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 4848 Z= 0.395 Angle : 0.871 13.195 6542 Z= 0.408 Chirality : 0.054 0.155 804 Planarity : 0.002 0.010 808 Dihedral : 10.797 76.329 748 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 3.95 % Allowed : 13.60 % Favored : 82.46 % 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: -4.03 (0.26), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.20), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS T 50 PHE 0.012 0.002 PHE I 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2402.19 seconds wall clock time: 43 minutes 47.36 seconds (2627.36 seconds total)