Starting phenix.real_space_refine on Wed May 14 10:01:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8thu_41272/05_2025/8thu_41272.cif Found real_map, /net/cci-nas-00/data/ceres_data/8thu_41272/05_2025/8thu_41272.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/8thu_41272/05_2025/8thu_41272.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8thu_41272/05_2025/8thu_41272.map" model { file = "/net/cci-nas-00/data/ceres_data/8thu_41272/05_2025/8thu_41272.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8thu_41272/05_2025/8thu_41272.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= 0.004 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 291 5.49 5 S 12 5.16 5 C 6569 2.51 5 N 2223 2.21 5 O 2807 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11902 Number of models: 1 Model: "" Number of chains: 10 Chain: "G" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 803 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 773 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 99} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 657 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 657 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Time building chain proxies: 7.45, per 1000 atoms: 0.63 Number of scatterers: 11902 At special positions: 0 Unit cell: (123.54, 124.392, 78.384, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 291 15.00 O 2807 8.00 N 2223 7.00 C 6569 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: 2.99 Conformation dependent library (CDL) restraints added in 926.7 milliseconds 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1424 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 7 sheets defined 71.2% alpha, 1.8% beta 144 base pairs and 254 stacking pairs defined. Time for finding SS restraints: 5.83 Creating SS restraints... Processing helix chain 'G' and resid 8 through 13 removed outlier: 3.838A pdb=" N ALA G 13 " --> pdb=" O ARG G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 28 Processing helix chain 'G' and resid 37 through 65 removed outlier: 3.799A pdb=" N ALA G 41 " --> pdb=" O GLY G 37 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL G 42 " --> pdb=" O ALA G 38 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU G 58 " --> pdb=" O GLU G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 83 Processing helix chain 'G' and resid 84 through 90 Processing helix chain 'C' and resid 8 through 13 removed outlier: 3.581A pdb=" N ALA C 13 " --> pdb=" O ARG C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 28 Processing helix chain 'C' and resid 37 through 66 removed outlier: 3.819A pdb=" N ALA C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL C 42 " --> pdb=" O ALA C 38 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 58 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 83 removed outlier: 3.513A pdb=" N LEU C 76 " --> pdb=" O THR C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 90 Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.771A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.727A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.062A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.619A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.559A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 Processing sheet with id=AA1, first strand: chain 'G' and resid 35 through 36 removed outlier: 7.232A pdb=" N ARG G 35 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'G' and resid 93 through 94 removed outlier: 6.243A pdb=" N THR G 93 " --> pdb=" O TYR B 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 35 through 36 removed outlier: 7.002A pdb=" N ARG C 35 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 93 through 94 removed outlier: 6.444A pdb=" N THR C 93 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.755A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 395 hydrogen bonds defined for protein. 1173 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 367 hydrogen bonds 734 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 254 stacking parallelities Total time for adding SS restraints: 4.05 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2785 1.34 - 1.46: 4202 1.46 - 1.58: 5121 1.58 - 1.70: 580 1.70 - 1.82: 22 Bond restraints: 12710 Sorted by residual: bond pdb=" N VAL D 69 " pdb=" CA VAL D 69 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.51e+00 bond pdb=" N VAL H 69 " pdb=" CA VAL H 69 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.40e+00 bond pdb=" N ASP C 83 " pdb=" CA ASP C 83 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.27e-02 6.20e+03 6.32e+00 bond pdb=" N GLU C 84 " pdb=" CA GLU C 84 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.28e-02 6.10e+03 5.57e+00 bond pdb=" N ASN D 67 " pdb=" CA ASN D 67 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.19e-02 7.06e+03 5.56e+00 ... (remaining 12705 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 18330 2.93 - 5.87: 82 5.87 - 8.80: 11 8.80 - 11.73: 4 11.73 - 14.66: 1 Bond angle restraints: 18428 Sorted by residual: angle pdb=" CB MET A 90 " pdb=" CG MET A 90 " pdb=" SD MET A 90 " ideal model delta sigma weight residual 112.70 127.36 -14.66 3.00e+00 1.11e-01 2.39e+01 angle pdb=" N GLY C 34 " pdb=" CA GLY C 34 " pdb=" C GLY C 34 " ideal model delta sigma weight residual 111.36 116.78 -5.42 1.17e+00 7.31e-01 2.14e+01 angle pdb=" CA LYS H 34 " pdb=" CB LYS H 34 " pdb=" CG LYS H 34 " ideal model delta sigma weight residual 114.10 123.27 -9.17 2.00e+00 2.50e-01 2.10e+01 angle pdb=" CA GLN C 11 " pdb=" CB GLN C 11 " pdb=" CG GLN C 11 " ideal model delta sigma weight residual 114.10 122.42 -8.32 2.00e+00 2.50e-01 1.73e+01 angle pdb=" CB LYS C 91 " pdb=" CG LYS C 91 " pdb=" CD LYS C 91 " ideal model delta sigma weight residual 111.30 120.23 -8.93 2.30e+00 1.89e-01 1.51e+01 ... (remaining 18423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.71: 5372 34.71 - 69.43: 1478 69.43 - 104.14: 17 104.14 - 138.86: 1 138.86 - 173.57: 2 Dihedral angle restraints: 6870 sinusoidal: 4666 harmonic: 2204 Sorted by residual: dihedral pdb=" CA THR C 31 " pdb=" C THR C 31 " pdb=" N SER C 32 " pdb=" CA SER C 32 " ideal model delta harmonic sigma weight residual 180.00 158.66 21.34 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" C4' DC J 3 " pdb=" C3' DC J 3 " pdb=" O3' DC J 3 " pdb=" P DG J 4 " ideal model delta sinusoidal sigma weight residual -140.00 33.57 -173.57 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT I 134 " pdb=" C3' DT I 134 " pdb=" O3' DT I 134 " pdb=" P DA I 135 " ideal model delta sinusoidal sigma weight residual 220.00 51.93 168.07 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 6867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1535 0.034 - 0.069: 440 0.069 - 0.103: 108 0.103 - 0.137: 27 0.137 - 0.171: 4 Chirality restraints: 2114 Sorted by residual: chirality pdb=" CA VAL H 69 " pdb=" N VAL H 69 " pdb=" C VAL H 69 " pdb=" CB VAL H 69 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.33e-01 chirality pdb=" CA VAL D 69 " pdb=" N VAL D 69 " pdb=" C VAL D 69 " pdb=" CB VAL D 69 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" P DA I 135 " pdb=" OP1 DA I 135 " pdb=" OP2 DA I 135 " pdb=" O5' DA I 135 " both_signs ideal model delta sigma weight residual True 2.35 -2.50 -0.15 2.00e-01 2.50e+01 5.76e-01 ... (remaining 2111 not shown) Planarity restraints: 1317 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 81 " 0.263 9.50e-02 1.11e+02 1.18e-01 8.56e+00 pdb=" NE ARG C 81 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG C 81 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 81 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 81 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP G 87 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.36e+00 pdb=" CG ASP G 87 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASP G 87 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP G 87 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 121 " -0.028 2.00e-02 2.50e+03 1.16e-02 4.03e+00 pdb=" N9 DG I 121 " 0.027 2.00e-02 2.50e+03 pdb=" C8 DG I 121 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 121 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG I 121 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 121 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 121 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DG I 121 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 121 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 121 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 121 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 121 " 0.002 2.00e-02 2.50e+03 ... (remaining 1314 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.20: 4 2.20 - 2.88: 3707 2.88 - 3.55: 16699 3.55 - 4.23: 31285 4.23 - 4.90: 47126 Nonbonded interactions: 98821 Sorted by model distance: nonbonded pdb=" NH1 ARG G 29 " pdb=" OE1 GLU H 71 " model vdw 1.528 3.120 nonbonded pdb=" NH2 ARG B 92 " pdb=" CD2 LEU D 101 " model vdw 1.954 3.540 nonbonded pdb=" CZ ARG G 29 " pdb=" OE1 GLU H 71 " model vdw 1.976 3.270 nonbonded pdb=" NH2 ARG G 29 " pdb=" OE1 GLU H 71 " model vdw 2.055 3.120 nonbonded pdb=" OG SER A 57 " pdb=" OE1 GLU A 59 " model vdw 2.208 3.040 ... (remaining 98816 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 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and (resid 6 through 66 or (resid 67 and (name N or name CA or name C \ or name O or name CB )) or resid 68 through 108)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 32 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 56 or (resid 57 through 58 and (na \ me N or name CA or name C or name O or name CB )) or resid 59 through 124)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 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: 0.450 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 32.970 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 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 : 0.004 0.052 12710 Z= 0.191 Angle : 0.681 14.663 18428 Z= 0.401 Chirality : 0.036 0.171 2114 Planarity : 0.006 0.118 1317 Dihedral : 28.562 173.573 5446 Min Nonbonded Distance : 1.528 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 18.48 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.30), residues: 744 helix: 2.07 (0.22), residues: 529 sheet: None (None), residues: 0 loop : -2.14 (0.34), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.008 0.001 PHE E 67 TYR 0.029 0.002 TYR D 83 ARG 0.010 0.000 ARG D 79 Details of bonding type rmsd hydrogen bonds : bond 0.10874 ( 762) hydrogen bonds : angle 3.34017 ( 1907) covalent geometry : bond 0.00393 (12710) covalent geometry : angle 0.68128 (18428) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.942 Fit side-chains REVERT: C 69 LYS cc_start: 0.8178 (ttmm) cc_final: 0.7608 (tttt) REVERT: D 68 ASP cc_start: 0.9168 (t0) cc_final: 0.8951 (t0) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.3404 time to fit residues: 58.5434 Evaluate side-chains 115 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.052558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.038777 restraints weight = 50828.663| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 1.90 r_work: 0.2642 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.0815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12710 Z= 0.186 Angle : 0.559 5.205 18428 Z= 0.339 Chirality : 0.033 0.129 2114 Planarity : 0.004 0.042 1317 Dihedral : 30.928 173.146 4024 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.27 % Allowed : 16.69 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.31), residues: 744 helix: 2.73 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -2.19 (0.36), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE B 61 TYR 0.020 0.001 TYR D 83 ARG 0.004 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.05002 ( 762) hydrogen bonds : angle 2.76507 ( 1907) covalent geometry : bond 0.00407 (12710) covalent geometry : angle 0.55861 (18428) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.934 Fit side-chains REVERT: G 47 ILE cc_start: 0.9616 (OUTLIER) cc_final: 0.9294 (mp) REVERT: C 11 GLN cc_start: 0.8981 (tm-30) cc_final: 0.8579 (tm-30) REVERT: C 69 LYS cc_start: 0.8505 (ttmm) cc_final: 0.8053 (tttm) REVERT: C 83 ASP cc_start: 0.7811 (t0) cc_final: 0.7454 (t0) REVERT: C 85 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8122 (mt-10) REVERT: E 115 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8872 (mtmm) REVERT: H 34 LYS cc_start: 0.8915 (mmpt) cc_final: 0.8612 (mmpt) REVERT: H 71 GLU cc_start: 0.8902 (tp30) cc_final: 0.8683 (mm-30) outliers start: 14 outliers final: 5 residues processed: 133 average time/residue: 0.3122 time to fit residues: 54.6744 Evaluate side-chains 127 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 4 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 27 optimal weight: 0.4980 chunk 76 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.051386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.037088 restraints weight = 50158.455| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 1.96 r_work: 0.2582 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 12710 Z= 0.269 Angle : 0.592 5.365 18428 Z= 0.358 Chirality : 0.036 0.137 2114 Planarity : 0.004 0.040 1317 Dihedral : 31.137 173.787 4024 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.76 % Allowed : 17.18 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.32), residues: 744 helix: 2.82 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -2.34 (0.36), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 49 PHE 0.010 0.001 PHE B 61 TYR 0.033 0.002 TYR D 83 ARG 0.003 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.06088 ( 762) hydrogen bonds : angle 2.99306 ( 1907) covalent geometry : bond 0.00607 (12710) covalent geometry : angle 0.59181 (18428) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.858 Fit side-chains REVERT: G 47 ILE cc_start: 0.9596 (OUTLIER) cc_final: 0.9253 (mp) REVERT: C 11 GLN cc_start: 0.9022 (tm-30) cc_final: 0.8516 (tm-30) REVERT: C 69 LYS cc_start: 0.8502 (ttmm) cc_final: 0.8030 (tttm) REVERT: E 115 LYS cc_start: 0.9324 (OUTLIER) cc_final: 0.8931 (mtmm) REVERT: H 34 LYS cc_start: 0.9010 (mmpt) cc_final: 0.8672 (mmpt) outliers start: 17 outliers final: 10 residues processed: 130 average time/residue: 0.3153 time to fit residues: 53.6865 Evaluate side-chains 124 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 65 optimal weight: 3.9990 chunk 64 optimal weight: 0.1980 chunk 85 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.052793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.038755 restraints weight = 50303.798| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 1.91 r_work: 0.2624 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12710 Z= 0.171 Angle : 0.540 5.299 18428 Z= 0.330 Chirality : 0.033 0.131 2114 Planarity : 0.004 0.040 1317 Dihedral : 30.801 174.308 4024 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.43 % Allowed : 17.67 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.32), residues: 744 helix: 2.97 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -2.18 (0.37), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.008 0.001 PHE E 67 TYR 0.029 0.001 TYR D 83 ARG 0.003 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.04546 ( 762) hydrogen bonds : angle 2.62822 ( 1907) covalent geometry : bond 0.00368 (12710) covalent geometry : angle 0.53990 (18428) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.839 Fit side-chains REVERT: G 47 ILE cc_start: 0.9618 (OUTLIER) cc_final: 0.9315 (mp) REVERT: C 11 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8507 (tm-30) REVERT: C 33 HIS cc_start: 0.8707 (OUTLIER) cc_final: 0.8349 (m170) REVERT: C 69 LYS cc_start: 0.8436 (ttmm) cc_final: 0.8055 (tttm) REVERT: C 83 ASP cc_start: 0.7989 (t0) cc_final: 0.7693 (t0) REVERT: C 87 ASP cc_start: 0.8686 (t0) cc_final: 0.8349 (t0) REVERT: C 91 LYS cc_start: 0.9394 (mmmt) cc_final: 0.9101 (mmtm) REVERT: D 71 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8788 (mm-30) REVERT: H 34 LYS cc_start: 0.9095 (mmpt) cc_final: 0.8803 (mmtt) outliers start: 15 outliers final: 8 residues processed: 135 average time/residue: 0.3034 time to fit residues: 54.0607 Evaluate side-chains 128 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain C residue 33 HIS Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 93 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.052002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.037961 restraints weight = 50636.365| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 1.92 r_work: 0.2609 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12710 Z= 0.228 Angle : 0.567 8.402 18428 Z= 0.343 Chirality : 0.034 0.133 2114 Planarity : 0.004 0.039 1317 Dihedral : 30.916 173.929 4024 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.92 % Allowed : 17.18 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.32), residues: 744 helix: 2.93 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -2.22 (0.37), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.008 0.001 PHE B 61 TYR 0.014 0.001 TYR D 83 ARG 0.006 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.05310 ( 762) hydrogen bonds : angle 2.78497 ( 1907) covalent geometry : bond 0.00510 (12710) covalent geometry : angle 0.56678 (18428) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.846 Fit side-chains REVERT: G 47 ILE cc_start: 0.9620 (OUTLIER) cc_final: 0.9273 (mp) REVERT: C 11 GLN cc_start: 0.9030 (tm-30) cc_final: 0.8343 (tm-30) REVERT: C 33 HIS cc_start: 0.8744 (OUTLIER) cc_final: 0.8415 (m170) REVERT: C 69 LYS cc_start: 0.8460 (ttmm) cc_final: 0.8062 (tttm) REVERT: C 83 ASP cc_start: 0.8090 (t0) cc_final: 0.7769 (t0) REVERT: C 87 ASP cc_start: 0.8700 (t0) cc_final: 0.8422 (t0) REVERT: C 91 LYS cc_start: 0.9429 (mmmt) cc_final: 0.9135 (mmtm) REVERT: D 86 ARG cc_start: 0.8885 (tpp80) cc_final: 0.8594 (tpp80) REVERT: E 115 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8861 (mtmm) REVERT: H 34 LYS cc_start: 0.9109 (mmpt) cc_final: 0.8851 (mmtt) outliers start: 18 outliers final: 10 residues processed: 131 average time/residue: 0.3610 time to fit residues: 63.1428 Evaluate side-chains 128 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain C residue 33 HIS Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 99 optimal weight: 7.9990 chunk 50 optimal weight: 0.1980 chunk 52 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.053872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.039878 restraints weight = 51607.124| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 1.90 r_work: 0.2665 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12710 Z= 0.154 Angle : 0.535 8.424 18428 Z= 0.325 Chirality : 0.032 0.130 2114 Planarity : 0.004 0.038 1317 Dihedral : 30.604 174.702 4024 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.62 % Allowed : 19.45 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.32), residues: 744 helix: 3.07 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -2.04 (0.38), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 113 PHE 0.007 0.001 PHE E 67 TYR 0.008 0.001 TYR D 121 ARG 0.006 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.04014 ( 762) hydrogen bonds : angle 2.47720 ( 1907) covalent geometry : bond 0.00327 (12710) covalent geometry : angle 0.53451 (18428) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.836 Fit side-chains REVERT: G 29 ARG cc_start: 0.8886 (tpp80) cc_final: 0.8658 (tpp80) REVERT: G 47 ILE cc_start: 0.9602 (OUTLIER) cc_final: 0.9300 (mp) REVERT: C 11 GLN cc_start: 0.9009 (tm-30) cc_final: 0.8344 (tm-30) REVERT: C 33 HIS cc_start: 0.8722 (OUTLIER) cc_final: 0.8382 (m170) REVERT: C 69 LYS cc_start: 0.8373 (ttmm) cc_final: 0.8009 (tttm) REVERT: C 83 ASP cc_start: 0.7953 (t0) cc_final: 0.7580 (t0) REVERT: C 87 ASP cc_start: 0.8666 (t0) cc_final: 0.8298 (t0) REVERT: C 91 LYS cc_start: 0.9409 (mmmt) cc_final: 0.9094 (mmtm) REVERT: A 50 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8357 (mt-10) REVERT: D 86 ARG cc_start: 0.8685 (tpp80) cc_final: 0.8453 (tpp80) REVERT: H 34 LYS cc_start: 0.9141 (mmpt) cc_final: 0.8886 (mmtt) outliers start: 10 outliers final: 6 residues processed: 136 average time/residue: 0.2926 time to fit residues: 53.0616 Evaluate side-chains 132 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain C residue 33 HIS Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 49 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 42 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.052446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.038430 restraints weight = 51150.933| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 1.92 r_work: 0.2619 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12710 Z= 0.216 Angle : 0.570 9.205 18428 Z= 0.343 Chirality : 0.034 0.130 2114 Planarity : 0.004 0.036 1317 Dihedral : 30.841 174.318 4024 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.62 % Allowed : 19.61 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.32), residues: 744 helix: 3.00 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -2.13 (0.38), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.009 0.001 PHE B 61 TYR 0.015 0.002 TYR D 121 ARG 0.005 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.05156 ( 762) hydrogen bonds : angle 2.73899 ( 1907) covalent geometry : bond 0.00481 (12710) covalent geometry : angle 0.57037 (18428) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.964 Fit side-chains REVERT: G 47 ILE cc_start: 0.9622 (OUTLIER) cc_final: 0.9277 (mp) REVERT: C 11 GLN cc_start: 0.9052 (tm-30) cc_final: 0.8366 (tm-30) REVERT: C 29 ARG cc_start: 0.7962 (mmm-85) cc_final: 0.7729 (mmm-85) REVERT: C 69 LYS cc_start: 0.8436 (ttmm) cc_final: 0.8041 (tttm) REVERT: C 87 ASP cc_start: 0.8710 (t0) cc_final: 0.8409 (t0) REVERT: C 91 LYS cc_start: 0.9440 (mmmt) cc_final: 0.9139 (mmtm) REVERT: D 71 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8653 (mm-30) outliers start: 10 outliers final: 7 residues processed: 129 average time/residue: 0.3079 time to fit residues: 52.5532 Evaluate side-chains 124 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 74 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.050951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.036694 restraints weight = 51203.637| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 1.94 r_work: 0.2562 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 12710 Z= 0.315 Angle : 0.632 6.802 18428 Z= 0.377 Chirality : 0.038 0.146 2114 Planarity : 0.004 0.036 1317 Dihedral : 31.185 173.344 4024 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.94 % Allowed : 19.45 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.32), residues: 744 helix: 2.76 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -2.35 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 49 PHE 0.010 0.001 PHE B 61 TYR 0.018 0.002 TYR D 83 ARG 0.006 0.000 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.06434 ( 762) hydrogen bonds : angle 3.08178 ( 1907) covalent geometry : bond 0.00714 (12710) covalent geometry : angle 0.63217 (18428) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.866 Fit side-chains REVERT: G 47 ILE cc_start: 0.9629 (OUTLIER) cc_final: 0.9277 (mp) REVERT: C 11 GLN cc_start: 0.9075 (tm-30) cc_final: 0.8367 (tm-30) REVERT: C 33 HIS cc_start: 0.8809 (OUTLIER) cc_final: 0.8513 (m170) REVERT: C 69 LYS cc_start: 0.8535 (ttmm) cc_final: 0.8126 (tttt) REVERT: C 87 ASP cc_start: 0.8733 (t0) cc_final: 0.8444 (t0) REVERT: C 91 LYS cc_start: 0.9462 (mmmt) cc_final: 0.9155 (mmtm) REVERT: H 76 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8705 (mm-30) outliers start: 12 outliers final: 8 residues processed: 123 average time/residue: 0.3139 time to fit residues: 50.9742 Evaluate side-chains 118 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain C residue 33 HIS Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 8 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 11 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.053098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.039177 restraints weight = 51092.386| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 1.92 r_work: 0.2649 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12710 Z= 0.168 Angle : 0.560 9.207 18428 Z= 0.337 Chirality : 0.033 0.131 2114 Planarity : 0.004 0.037 1317 Dihedral : 30.728 173.791 4024 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.62 % Allowed : 19.94 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.32), residues: 744 helix: 3.06 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -2.10 (0.38), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 113 PHE 0.007 0.001 PHE F 61 TYR 0.012 0.001 TYR D 83 ARG 0.005 0.000 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.04445 ( 762) hydrogen bonds : angle 2.58336 ( 1907) covalent geometry : bond 0.00364 (12710) covalent geometry : angle 0.56043 (18428) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 1.174 Fit side-chains revert: symmetry clash REVERT: G 47 ILE cc_start: 0.9600 (OUTLIER) cc_final: 0.9295 (mp) REVERT: C 11 GLN cc_start: 0.9039 (tm-30) cc_final: 0.8336 (tm-30) REVERT: C 29 ARG cc_start: 0.7945 (mmm-85) cc_final: 0.7675 (mmm-85) REVERT: C 33 HIS cc_start: 0.8756 (OUTLIER) cc_final: 0.8450 (m170) REVERT: C 69 LYS cc_start: 0.8409 (ttmm) cc_final: 0.8031 (tttm) REVERT: C 87 ASP cc_start: 0.8644 (t0) cc_final: 0.8348 (t0) REVERT: C 91 LYS cc_start: 0.9419 (mmmt) cc_final: 0.9115 (mmtm) REVERT: A 50 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8379 (mt-10) REVERT: D 71 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8609 (mm-30) outliers start: 10 outliers final: 8 residues processed: 127 average time/residue: 0.3020 time to fit residues: 51.9443 Evaluate side-chains 128 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain C residue 33 HIS Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 47 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 9 optimal weight: 0.0980 chunk 54 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.053816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.039912 restraints weight = 50797.144| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 1.88 r_work: 0.2666 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12710 Z= 0.154 Angle : 0.559 10.918 18428 Z= 0.333 Chirality : 0.032 0.129 2114 Planarity : 0.004 0.037 1317 Dihedral : 30.634 174.505 4024 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.30 % Allowed : 20.58 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.32), residues: 744 helix: 3.09 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -1.94 (0.38), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.007 0.001 PHE F 61 TYR 0.007 0.001 TYR D 121 ARG 0.004 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.04057 ( 762) hydrogen bonds : angle 2.49575 ( 1907) covalent geometry : bond 0.00331 (12710) covalent geometry : angle 0.55897 (18428) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: G 47 ILE cc_start: 0.9602 (OUTLIER) cc_final: 0.9303 (mp) REVERT: C 11 GLN cc_start: 0.9003 (tm-30) cc_final: 0.8369 (tm-30) REVERT: C 29 ARG cc_start: 0.7895 (mmm-85) cc_final: 0.7651 (mmm-85) REVERT: C 33 HIS cc_start: 0.8685 (OUTLIER) cc_final: 0.8364 (m170) REVERT: C 69 LYS cc_start: 0.8340 (ttmm) cc_final: 0.7997 (tttm) REVERT: A 50 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8384 (mt-10) REVERT: D 71 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8586 (mm-30) outliers start: 8 outliers final: 5 residues processed: 127 average time/residue: 0.2940 time to fit residues: 49.8221 Evaluate side-chains 125 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain C residue 33 HIS Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 75 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 72 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.051454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.037255 restraints weight = 50603.854| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 1.91 r_work: 0.2580 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 12710 Z= 0.292 Angle : 0.631 7.848 18428 Z= 0.374 Chirality : 0.037 0.140 2114 Planarity : 0.004 0.035 1317 Dihedral : 31.066 173.745 4024 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.78 % Allowed : 19.94 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.32), residues: 744 helix: 2.84 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -2.23 (0.38), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 49 PHE 0.009 0.001 PHE B 61 TYR 0.026 0.002 TYR D 83 ARG 0.004 0.001 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.06119 ( 762) hydrogen bonds : angle 2.99210 ( 1907) covalent geometry : bond 0.00663 (12710) covalent geometry : angle 0.63138 (18428) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4735.24 seconds wall clock time: 82 minutes 38.29 seconds (4958.29 seconds total)