Starting phenix.real_space_refine on Sun Apr 7 23:45:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6px1_20516/04_2024/6px1_20516.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6px1_20516/04_2024/6px1_20516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6px1_20516/04_2024/6px1_20516.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6px1_20516/04_2024/6px1_20516.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6px1_20516/04_2024/6px1_20516.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6px1_20516/04_2024/6px1_20516.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 290 5.49 5 S 12 5.16 5 C 6594 2.51 5 N 2249 2.21 5 O 2792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H GLU 68": "OE1" <-> "OE2" Residue "H GLU 110": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 11937 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 792 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 752 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 792 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 752 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2957 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2988 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Time building chain proxies: 6.99, per 1000 atoms: 0.59 Number of scatterers: 11937 At special positions: 0 Unit cell: (73.84, 117.52, 114.4, 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 290 15.00 O 2792 8.00 N 2249 7.00 C 6594 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.64 Conformation dependent library (CDL) restraints added in 1.2 seconds 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1408 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 10 sheets defined 70.9% alpha, 3.2% beta 143 base pairs and 274 stacking pairs defined. Time for finding SS restraints: 6.05 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.672A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 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: 3.668A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.578A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.613A pdb=" N ILE C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.553A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 102 through 120 removed outlier: 3.835A pdb=" N VAL D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.694A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) 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 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.764A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.339A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.530A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.612A pdb=" N LEU G 116 " --> pdb=" O SER G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.521A pdb=" N ARG H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 102 through 120 removed outlier: 3.863A pdb=" N VAL H 108 " --> pdb=" O ALA H 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.765A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.412A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.154A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.904A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.272A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 376 hydrogen bonds defined for protein. 1113 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 368 hydrogen bonds 736 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 274 stacking parallelities Total time for adding SS restraints: 4.12 Time building geometry restraints manager: 6.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2040 1.33 - 1.45: 4253 1.45 - 1.57: 5847 1.57 - 1.68: 578 1.68 - 1.80: 22 Bond restraints: 12740 Sorted by residual: bond pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " ideal model delta sigma weight residual 1.422 1.490 -0.068 3.00e-02 1.11e+03 5.12e+00 bond pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " ideal model delta sigma weight residual 1.422 1.490 -0.068 3.00e-02 1.11e+03 5.10e+00 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.422 1.485 -0.063 3.00e-02 1.11e+03 4.40e+00 bond pdb=" CG1 ILE D 58 " pdb=" CD1 ILE D 58 " ideal model delta sigma weight residual 1.513 1.437 0.076 3.90e-02 6.57e+02 3.79e+00 bond pdb=" CG1 ILE H 58 " pdb=" CD1 ILE H 58 " ideal model delta sigma weight residual 1.513 1.439 0.074 3.90e-02 6.57e+02 3.64e+00 ... (remaining 12735 not shown) Histogram of bond angle deviations from ideal: 98.33 - 105.37: 1361 105.37 - 112.40: 6913 112.40 - 119.43: 3944 119.43 - 126.47: 5353 126.47 - 133.50: 876 Bond angle restraints: 18447 Sorted by residual: angle pdb=" C GLU G 64 " pdb=" CA GLU G 64 " pdb=" CB GLU G 64 " ideal model delta sigma weight residual 110.90 102.08 8.82 1.58e+00 4.01e-01 3.12e+01 angle pdb=" N GLU D 32 " pdb=" CA GLU D 32 " pdb=" C GLU D 32 " ideal model delta sigma weight residual 108.58 117.83 -9.25 1.82e+00 3.02e-01 2.58e+01 angle pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " pdb=" P DC J 127 " ideal model delta sigma weight residual 120.20 126.32 -6.12 1.50e+00 4.44e-01 1.66e+01 angle pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " pdb=" P DG J 95 " ideal model delta sigma weight residual 120.20 126.09 -5.89 1.50e+00 4.44e-01 1.54e+01 angle pdb=" N ARG D 30 " pdb=" CA ARG D 30 " pdb=" C ARG D 30 " ideal model delta sigma weight residual 109.71 114.76 -5.05 1.41e+00 5.03e-01 1.28e+01 ... (remaining 18442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.51: 5436 35.51 - 71.02: 1476 71.02 - 106.54: 5 106.54 - 142.05: 0 142.05 - 177.56: 3 Dihedral angle restraints: 6920 sinusoidal: 4738 harmonic: 2182 Sorted by residual: dihedral pdb=" CA PRO G 117 " pdb=" C PRO G 117 " pdb=" N LYS G 118 " pdb=" CA LYS G 118 " ideal model delta harmonic sigma weight residual 180.00 -154.87 -25.13 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA LYS D 31 " pdb=" C LYS D 31 " pdb=" N GLU D 32 " pdb=" CA GLU D 32 " ideal model delta harmonic sigma weight residual 180.00 159.46 20.54 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" C4' DT J 15 " pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sinusoidal sigma weight residual -140.00 37.56 -177.56 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 6917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1618 0.056 - 0.112: 410 0.112 - 0.168: 56 0.168 - 0.224: 11 0.224 - 0.280: 3 Chirality restraints: 2098 Sorted by residual: chirality pdb=" CA ILE G 79 " pdb=" N ILE G 79 " pdb=" C ILE G 79 " pdb=" CB ILE G 79 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA THR A 45 " pdb=" N THR A 45 " pdb=" C THR A 45 " pdb=" CB THR A 45 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C3' DC J 126 " pdb=" C4' DC J 126 " pdb=" O3' DC J 126 " pdb=" C2' DC J 126 " both_signs ideal model delta sigma weight residual False -2.66 -2.44 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 2095 not shown) Planarity restraints: 1330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 68 " -0.022 2.00e-02 2.50e+03 4.39e-02 1.93e+01 pdb=" C GLU D 68 " 0.076 2.00e-02 2.50e+03 pdb=" O GLU D 68 " -0.028 2.00e-02 2.50e+03 pdb=" N ARG D 69 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 64 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.26e+00 pdb=" C ASN F 64 " -0.053 2.00e-02 2.50e+03 pdb=" O ASN F 64 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL F 65 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 80 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.77e+00 pdb=" C THR F 80 " -0.051 2.00e-02 2.50e+03 pdb=" O THR F 80 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL F 81 " 0.017 2.00e-02 2.50e+03 ... (remaining 1327 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1790 2.76 - 3.30: 9452 3.30 - 3.83: 23879 3.83 - 4.37: 28890 4.37 - 4.90: 40918 Nonbonded interactions: 104929 Sorted by model distance: nonbonded pdb=" OG SER A 57 " pdb=" OE1 GLU A 59 " model vdw 2.228 2.440 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.287 2.440 nonbonded pdb=" O HIS F 75 " pdb=" NH2 ARG H 89 " model vdw 2.308 2.520 nonbonded pdb=" OE1 GLN F 93 " pdb=" NH2 ARG F 95 " model vdw 2.319 2.520 nonbonded pdb=" O TYR G 39 " pdb=" OG SER H 75 " model vdw 2.329 2.440 ... (remaining 104924 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 2.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.990 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 39.630 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 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 : 0.006 0.076 12740 Z= 0.350 Angle : 0.867 9.252 18447 Z= 0.524 Chirality : 0.050 0.280 2098 Planarity : 0.008 0.068 1330 Dihedral : 28.550 177.562 5512 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % 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: -2.98 (0.24), residues: 736 helix: -1.77 (0.18), residues: 528 sheet: None (None), residues: 0 loop : -2.02 (0.34), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.019 0.003 PHE C 25 TYR 0.024 0.003 TYR E 41 ARG 0.014 0.001 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.877 Fit side-chains REVERT: F 25 ASN cc_start: 0.8710 (m-40) cc_final: 0.8491 (m-40) REVERT: F 35 ARG cc_start: 0.8441 (mtp85) cc_final: 0.8052 (mtm110) REVERT: G 42 ARG cc_start: 0.8342 (ptp-170) cc_final: 0.8052 (mtm180) REVERT: G 94 ASN cc_start: 0.8630 (t0) cc_final: 0.8325 (t0) REVERT: H 87 THR cc_start: 0.8363 (p) cc_final: 0.8141 (t) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.4633 time to fit residues: 94.0284 Evaluate side-chains 129 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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: 6.9990 chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 58 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 108 ASN B 25 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN E 68 GLN F 25 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12740 Z= 0.192 Angle : 0.563 10.634 18447 Z= 0.342 Chirality : 0.034 0.175 2098 Planarity : 0.005 0.053 1330 Dihedral : 30.881 174.037 4008 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 0.95 % Allowed : 11.27 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.29), residues: 736 helix: 0.37 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -1.33 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.012 0.001 PHE E 67 TYR 0.009 0.001 TYR A 54 ARG 0.004 0.000 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 133 time to evaluate : 0.926 Fit side-chains REVERT: B 72 TYR cc_start: 0.8771 (m-80) cc_final: 0.8515 (m-80) REVERT: E 59 GLU cc_start: 0.7403 (mp0) cc_final: 0.6967 (mp0) REVERT: E 73 GLU cc_start: 0.6960 (tt0) cc_final: 0.6738 (tt0) REVERT: F 25 ASN cc_start: 0.8669 (m110) cc_final: 0.8226 (m-40) outliers start: 6 outliers final: 2 residues processed: 134 average time/residue: 0.4162 time to fit residues: 70.1235 Evaluate side-chains 125 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 123 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain D residue 85 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 31 optimal weight: 0.5980 chunk 72 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 25 ASN B 75 HIS C 68 ASN C 73 ASN D 44 GLN D 92 GLN E 76 GLN E 113 HIS F 75 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 12740 Z= 0.353 Angle : 0.616 9.354 18447 Z= 0.364 Chirality : 0.038 0.172 2098 Planarity : 0.005 0.045 1330 Dihedral : 31.398 172.345 4008 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.06 % Allowed : 11.59 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.30), residues: 736 helix: 0.83 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -1.11 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 75 PHE 0.014 0.002 PHE E 67 TYR 0.012 0.002 TYR D 118 ARG 0.005 0.001 ARG G 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 128 time to evaluate : 0.873 Fit side-chains REVERT: A 56 LYS cc_start: 0.8424 (ttpp) cc_final: 0.8020 (ttpp) REVERT: A 87 SER cc_start: 0.9020 (p) cc_final: 0.8782 (p) REVERT: E 59 GLU cc_start: 0.7629 (mp0) cc_final: 0.7340 (mp0) REVERT: E 73 GLU cc_start: 0.7059 (tt0) cc_final: 0.6852 (tt0) REVERT: F 25 ASN cc_start: 0.8667 (m110) cc_final: 0.8295 (m-40) REVERT: F 85 ASP cc_start: 0.8030 (m-30) cc_final: 0.7762 (m-30) REVERT: H 54 LYS cc_start: 0.8474 (mmmt) cc_final: 0.8163 (mmtt) outliers start: 13 outliers final: 13 residues processed: 131 average time/residue: 0.3694 time to fit residues: 62.5081 Evaluate side-chains 132 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 119 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12740 Z= 0.176 Angle : 0.537 11.391 18447 Z= 0.322 Chirality : 0.033 0.165 2098 Planarity : 0.004 0.046 1330 Dihedral : 30.732 176.603 4008 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.63 % Allowed : 13.65 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.31), residues: 736 helix: 1.71 (0.23), residues: 538 sheet: None (None), residues: 0 loop : -0.74 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 75 PHE 0.011 0.001 PHE E 67 TYR 0.009 0.001 TYR D 118 ARG 0.004 0.000 ARG G 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 125 time to evaluate : 0.918 Fit side-chains REVERT: A 59 GLU cc_start: 0.7594 (mp0) cc_final: 0.7237 (pm20) REVERT: A 87 SER cc_start: 0.8969 (p) cc_final: 0.8755 (p) REVERT: B 84 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7177 (mmt) REVERT: C 24 GLN cc_start: 0.8179 (mm110) cc_final: 0.7950 (mm-40) REVERT: D 90 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7374 (mp0) REVERT: E 59 GLU cc_start: 0.7562 (mp0) cc_final: 0.7226 (mp0) REVERT: F 25 ASN cc_start: 0.8665 (m110) cc_final: 0.8315 (m-40) outliers start: 4 outliers final: 1 residues processed: 127 average time/residue: 0.3366 time to fit residues: 56.3294 Evaluate side-chains 120 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 117 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 90 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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** C 24 GLN E 108 ASN G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12740 Z= 0.211 Angle : 0.545 11.286 18447 Z= 0.325 Chirality : 0.034 0.160 2098 Planarity : 0.004 0.044 1330 Dihedral : 30.796 177.083 4008 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.43 % Allowed : 14.44 % Favored : 84.13 % 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: 1.83 (0.31), residues: 736 helix: 1.89 (0.23), residues: 538 sheet: None (None), residues: 0 loop : -0.67 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 75 PHE 0.010 0.001 PHE E 67 TYR 0.018 0.001 TYR D 118 ARG 0.003 0.000 ARG G 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 0.833 Fit side-chains REVERT: A 59 GLU cc_start: 0.7660 (mp0) cc_final: 0.7298 (pm20) REVERT: A 87 SER cc_start: 0.8962 (p) cc_final: 0.8746 (p) REVERT: B 84 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7274 (mmt) REVERT: C 24 GLN cc_start: 0.8185 (mm-40) cc_final: 0.7979 (mm-40) REVERT: D 90 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7416 (mp0) REVERT: E 59 GLU cc_start: 0.7575 (mp0) cc_final: 0.7273 (mp0) outliers start: 9 outliers final: 5 residues processed: 122 average time/residue: 0.3436 time to fit residues: 55.1156 Evaluate side-chains 124 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 117 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 0.0870 chunk 50 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN E 76 GLN E 108 ASN F 25 ASN G 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12740 Z= 0.183 Angle : 0.537 11.019 18447 Z= 0.321 Chirality : 0.033 0.152 2098 Planarity : 0.004 0.045 1330 Dihedral : 30.766 177.558 4008 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.59 % Allowed : 14.92 % Favored : 83.49 % 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: 2.05 (0.32), residues: 736 helix: 2.07 (0.23), residues: 538 sheet: None (None), residues: 0 loop : -0.65 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 75 PHE 0.009 0.001 PHE E 67 TYR 0.015 0.001 TYR D 118 ARG 0.004 0.000 ARG G 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 119 time to evaluate : 1.009 Fit side-chains REVERT: A 59 GLU cc_start: 0.7632 (mp0) cc_final: 0.7339 (pm20) REVERT: A 87 SER cc_start: 0.8955 (p) cc_final: 0.8749 (p) REVERT: B 84 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7229 (mmt) REVERT: C 24 GLN cc_start: 0.8105 (mm-40) cc_final: 0.7791 (mm-40) REVERT: D 30 ARG cc_start: 0.7398 (ttt90) cc_final: 0.6926 (ttm-80) REVERT: D 32 GLU cc_start: 0.7118 (mp0) cc_final: 0.6278 (mp0) REVERT: D 37 TYR cc_start: 0.8949 (m-80) cc_final: 0.8370 (m-80) REVERT: D 90 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7413 (mp0) REVERT: E 59 GLU cc_start: 0.7607 (mp0) cc_final: 0.7301 (mp0) outliers start: 10 outliers final: 8 residues processed: 121 average time/residue: 0.3517 time to fit residues: 55.8368 Evaluate side-chains 125 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 5.9990 chunk 70 optimal weight: 0.4980 chunk 54 optimal weight: 0.5980 chunk 81 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 44 optimal weight: 0.0050 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN F 25 ASN G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12740 Z= 0.159 Angle : 0.530 11.122 18447 Z= 0.317 Chirality : 0.032 0.151 2098 Planarity : 0.004 0.045 1330 Dihedral : 30.667 178.151 4008 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.59 % Allowed : 15.56 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.32), residues: 736 helix: 2.30 (0.23), residues: 538 sheet: None (None), residues: 0 loop : -0.59 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 75 PHE 0.009 0.001 PHE A 67 TYR 0.015 0.001 TYR D 118 ARG 0.004 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 114 time to evaluate : 0.791 Fit side-chains REVERT: A 59 GLU cc_start: 0.7657 (mp0) cc_final: 0.7341 (pm20) REVERT: B 84 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7166 (mmt) REVERT: B 92 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8303 (ptm-80) REVERT: C 24 GLN cc_start: 0.8142 (mm-40) cc_final: 0.7862 (mm-40) REVERT: D 30 ARG cc_start: 0.7425 (ttt90) cc_final: 0.6979 (ttm-80) REVERT: D 32 GLU cc_start: 0.7113 (mp0) cc_final: 0.6287 (mp0) REVERT: D 37 TYR cc_start: 0.8951 (m-80) cc_final: 0.8375 (m-80) REVERT: D 83 ARG cc_start: 0.8223 (mmt90) cc_final: 0.7988 (mmt-90) REVERT: D 90 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7366 (mp0) REVERT: E 59 GLU cc_start: 0.7567 (mp0) cc_final: 0.7302 (mp0) REVERT: H 43 LYS cc_start: 0.8639 (mmtt) cc_final: 0.8368 (mmtt) REVERT: H 87 THR cc_start: 0.8373 (OUTLIER) cc_final: 0.8108 (t) outliers start: 10 outliers final: 4 residues processed: 118 average time/residue: 0.3668 time to fit residues: 56.1423 Evaluate side-chains 120 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.0970 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 0.0060 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 overall best weight: 1.0198 ------------------------------------------------------------------------------- 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** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN F 25 ASN G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12740 Z= 0.186 Angle : 0.537 11.592 18447 Z= 0.319 Chirality : 0.033 0.152 2098 Planarity : 0.004 0.044 1330 Dihedral : 30.677 178.321 4008 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.90 % Allowed : 15.24 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.31), residues: 736 helix: 2.34 (0.23), residues: 538 sheet: None (None), residues: 0 loop : -0.57 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 75 PHE 0.009 0.001 PHE E 67 TYR 0.017 0.001 TYR D 118 ARG 0.004 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 0.976 Fit side-chains REVERT: A 59 GLU cc_start: 0.7542 (mp0) cc_final: 0.7306 (pm20) REVERT: A 87 SER cc_start: 0.8955 (p) cc_final: 0.8751 (p) REVERT: B 84 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7203 (mmt) REVERT: B 92 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8296 (ptm-80) REVERT: C 24 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7817 (mm-40) REVERT: D 30 ARG cc_start: 0.7434 (ttt90) cc_final: 0.7055 (ttm-80) REVERT: D 32 GLU cc_start: 0.7189 (mp0) cc_final: 0.6388 (mp0) REVERT: D 37 TYR cc_start: 0.8958 (m-80) cc_final: 0.8391 (m-80) REVERT: D 83 ARG cc_start: 0.8238 (mmt90) cc_final: 0.8011 (mmt-90) REVERT: D 90 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: E 59 GLU cc_start: 0.7573 (mp0) cc_final: 0.7315 (mp0) REVERT: H 54 LYS cc_start: 0.8449 (mmmt) cc_final: 0.8178 (mmtt) outliers start: 12 outliers final: 9 residues processed: 119 average time/residue: 0.3633 time to fit residues: 56.2156 Evaluate side-chains 128 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 44 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 70 optimal weight: 0.0070 chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 overall best weight: 1.5202 ------------------------------------------------------------------------------- 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** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12740 Z= 0.226 Angle : 0.550 12.075 18447 Z= 0.324 Chirality : 0.034 0.154 2098 Planarity : 0.004 0.043 1330 Dihedral : 30.851 178.466 4008 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.06 % Allowed : 15.24 % Favored : 82.70 % 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: 2.32 (0.31), residues: 736 helix: 2.35 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -0.66 (0.41), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.009 0.001 PHE A 67 TYR 0.019 0.001 TYR D 118 ARG 0.004 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 120 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7582 (mp0) cc_final: 0.7355 (pm20) REVERT: A 87 SER cc_start: 0.8950 (p) cc_final: 0.8737 (p) REVERT: B 84 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7394 (mmt) REVERT: B 92 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8332 (ptm-80) REVERT: D 32 GLU cc_start: 0.7213 (mp0) cc_final: 0.6479 (mp0) REVERT: D 90 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7425 (mp0) REVERT: E 59 GLU cc_start: 0.7612 (mp0) cc_final: 0.7327 (mp0) REVERT: H 54 LYS cc_start: 0.8449 (mmmt) cc_final: 0.8194 (mmtt) outliers start: 13 outliers final: 9 residues processed: 123 average time/residue: 0.3699 time to fit residues: 58.7589 Evaluate side-chains 128 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 44 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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** D 46 HIS E 76 GLN F 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12740 Z= 0.215 Angle : 0.552 12.749 18447 Z= 0.325 Chirality : 0.034 0.154 2098 Planarity : 0.004 0.043 1330 Dihedral : 30.841 178.655 4008 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.70 % Allowed : 15.08 % Favored : 82.22 % 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: 2.35 (0.31), residues: 736 helix: 2.36 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -0.60 (0.42), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.009 0.001 PHE E 67 TYR 0.018 0.001 TYR D 118 ARG 0.007 0.000 ARG H 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 119 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7614 (mp0) cc_final: 0.7357 (pm20) REVERT: A 87 SER cc_start: 0.8943 (p) cc_final: 0.8737 (p) REVERT: B 84 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7349 (mmt) REVERT: B 92 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8311 (ptm-80) REVERT: D 32 GLU cc_start: 0.7229 (mp0) cc_final: 0.6518 (mp0) REVERT: D 90 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: E 59 GLU cc_start: 0.7603 (mp0) cc_final: 0.7335 (mp0) REVERT: F 84 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7339 (mmt) REVERT: H 54 LYS cc_start: 0.8424 (mmmt) cc_final: 0.8164 (mmtt) REVERT: H 56 MET cc_start: 0.8422 (tpp) cc_final: 0.7833 (tpt) REVERT: H 90 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7252 (mt-10) outliers start: 17 outliers final: 11 residues processed: 125 average time/residue: 0.3650 time to fit residues: 59.6590 Evaluate side-chains 130 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 7.9990 chunk 11 optimal weight: 0.0470 chunk 22 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 33 optimal weight: 0.4980 chunk 81 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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** C 73 ASN C 104 GLN D 46 HIS E 76 GLN E 108 ASN F 25 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.145966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.104040 restraints weight = 17651.931| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.41 r_work: 0.3171 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12740 Z= 0.161 Angle : 0.538 12.736 18447 Z= 0.317 Chirality : 0.032 0.179 2098 Planarity : 0.003 0.039 1330 Dihedral : 30.549 179.700 4008 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.43 % Allowed : 16.51 % Favored : 82.06 % 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: 2.66 (0.31), residues: 736 helix: 2.52 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -0.36 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 46 PHE 0.012 0.001 PHE E 78 TYR 0.015 0.001 TYR D 118 ARG 0.006 0.000 ARG H 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2283.86 seconds wall clock time: 42 minutes 23.92 seconds (2543.92 seconds total)