Starting phenix.real_space_refine on Tue Mar 3 20:44:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zhy_11221/03_2026/6zhy_11221.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zhy_11221/03_2026/6zhy_11221.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6zhy_11221/03_2026/6zhy_11221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zhy_11221/03_2026/6zhy_11221.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zhy_11221/03_2026/6zhy_11221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zhy_11221/03_2026/6zhy_11221.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 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 218 5.49 5 S 8 5.16 5 C 4968 2.51 5 N 1700 2.21 5 O 2105 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8999 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 673 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "C" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 813 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "I" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 2236 Classifications: {'DNA': 110} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 109} Chain: "J" Number of atoms: 2268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 2268 Classifications: {'DNA': 110} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 109} Chain: "K" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Time building chain proxies: 1.90, per 1000 atoms: 0.21 Number of scatterers: 8999 At special positions: 0 Unit cell: (115.758, 107.256, 101.37, 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 8 16.00 P 218 15.00 O 2105 8.00 N 1700 7.00 C 4968 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: 0.63 Conformation dependent library (CDL) restraints added in 132.0 milliseconds 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1052 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 7 sheets defined 73.5% alpha, 2.5% beta 110 base pairs and 196 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 4.097A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.860A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.787A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.400A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 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 100 through 121 removed outlier: 3.588A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.818A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.663A 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 'C' and resid 42 through 43 removed outlier: 7.157A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.620A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.472A 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 119 306 hydrogen bonds defined for protein. 894 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 285 hydrogen bonds 570 hydrogen bond angles 0 basepair planarities 110 basepair parallelities 196 stacking parallelities Total time for adding SS restraints: 1.51 Time building geometry restraints manager: 0.83 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: 1561 1.33 - 1.45: 3291 1.45 - 1.57: 4300 1.57 - 1.69: 437 1.69 - 1.81: 16 Bond restraints: 9605 Sorted by residual: bond pdb=" C3' DC I 6 " pdb=" C2' DC I 6 " ideal model delta sigma weight residual 1.525 1.562 -0.037 2.00e-02 2.50e+03 3.43e+00 bond pdb=" C3' DT J 69 " pdb=" C2' DT J 69 " ideal model delta sigma weight residual 1.525 1.561 -0.036 2.00e-02 2.50e+03 3.29e+00 bond pdb=" C3' DC I 4 " pdb=" C2' DC I 4 " ideal model delta sigma weight residual 1.525 1.561 -0.036 2.00e-02 2.50e+03 3.27e+00 bond pdb=" CB PRO A 38 " pdb=" CG PRO A 38 " ideal model delta sigma weight residual 1.492 1.574 -0.082 5.00e-02 4.00e+02 2.67e+00 bond pdb=" C3' DG J -19 " pdb=" C2' DG J -19 " ideal model delta sigma weight residual 1.525 1.557 -0.032 2.00e-02 2.50e+03 2.63e+00 ... (remaining 9600 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 12009 1.20 - 2.40: 1415 2.40 - 3.60: 382 3.60 - 4.80: 81 4.80 - 6.00: 20 Bond angle restraints: 13907 Sorted by residual: angle pdb=" O3' DT J -17 " pdb=" C3' DT J -17 " pdb=" C2' DT J -17 " ideal model delta sigma weight residual 111.50 117.50 -6.00 1.50e+00 4.44e-01 1.60e+01 angle pdb=" C4' DT I 30 " pdb=" O4' DT I 30 " pdb=" C1' DT I 30 " ideal model delta sigma weight residual 109.70 103.81 5.89 1.50e+00 4.44e-01 1.54e+01 angle pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sigma weight residual 120.20 125.97 -5.77 1.50e+00 4.44e-01 1.48e+01 angle pdb=" O4' DG I 26 " pdb=" C1' DG I 26 " pdb=" N9 DG I 26 " ideal model delta sigma weight residual 108.40 102.78 5.62 1.50e+00 4.44e-01 1.41e+01 angle pdb=" O4' DG I 28 " pdb=" C1' DG I 28 " pdb=" N9 DG I 28 " ideal model delta sigma weight residual 108.40 102.99 5.41 1.50e+00 4.44e-01 1.30e+01 ... (remaining 13902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.42: 4197 33.42 - 66.83: 967 66.83 - 100.25: 36 100.25 - 133.66: 0 133.66 - 167.07: 2 Dihedral angle restraints: 5202 sinusoidal: 3573 harmonic: 1629 Sorted by residual: dihedral pdb=" CA PRO D 100 " pdb=" C PRO D 100 " pdb=" N GLY D 101 " pdb=" CA GLY D 101 " ideal model delta harmonic sigma weight residual 180.00 153.18 26.82 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA THR D 85 " pdb=" C THR D 85 " pdb=" N ILE D 86 " pdb=" CA ILE D 86 " ideal model delta harmonic sigma weight residual 180.00 157.65 22.35 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA PHE E 84 " pdb=" C PHE E 84 " pdb=" N GLN E 85 " pdb=" CA GLN E 85 " ideal model delta harmonic sigma weight residual 180.00 160.31 19.69 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 5199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1285 0.068 - 0.136: 245 0.136 - 0.204: 25 0.204 - 0.273: 18 0.273 - 0.341: 6 Chirality restraints: 1579 Sorted by residual: chirality pdb=" C4' DT J 69 " pdb=" C5' DT J 69 " pdb=" O4' DT J 69 " pdb=" C3' DT J 69 " both_signs ideal model delta sigma weight residual False -2.53 -2.18 -0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" C4' DC I 4 " pdb=" C5' DC I 4 " pdb=" O4' DC I 4 " pdb=" C3' DC I 4 " both_signs ideal model delta sigma weight residual False -2.53 -2.22 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" C3' DG J 20 " pdb=" C4' DG J 20 " pdb=" O3' DG J 20 " pdb=" C2' DG J 20 " both_signs ideal model delta sigma weight residual False -2.66 -2.37 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 1576 not shown) Planarity restraints: 999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I 6 " -0.063 2.00e-02 2.50e+03 3.45e-02 2.67e+01 pdb=" N1 DC I 6 " 0.075 2.00e-02 2.50e+03 pdb=" C2 DC I 6 " -0.016 2.00e-02 2.50e+03 pdb=" O2 DC I 6 " 0.018 2.00e-02 2.50e+03 pdb=" N3 DC I 6 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DC I 6 " -0.007 2.00e-02 2.50e+03 pdb=" N4 DC I 6 " -0.020 2.00e-02 2.50e+03 pdb=" C5 DC I 6 " 0.008 2.00e-02 2.50e+03 pdb=" C6 DC I 6 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 4 " -0.053 2.00e-02 2.50e+03 3.09e-02 2.14e+01 pdb=" N1 DC I 4 " 0.071 2.00e-02 2.50e+03 pdb=" C2 DC I 4 " -0.017 2.00e-02 2.50e+03 pdb=" O2 DC I 4 " 0.013 2.00e-02 2.50e+03 pdb=" N3 DC I 4 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 4 " -0.005 2.00e-02 2.50e+03 pdb=" N4 DC I 4 " -0.014 2.00e-02 2.50e+03 pdb=" C5 DC I 4 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DC I 4 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 19 " -0.042 2.00e-02 2.50e+03 2.86e-02 1.84e+01 pdb=" N1 DC J 19 " 0.069 2.00e-02 2.50e+03 pdb=" C2 DC J 19 " -0.025 2.00e-02 2.50e+03 pdb=" O2 DC J 19 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DC J 19 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DC J 19 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC J 19 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DC J 19 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DC J 19 " 0.002 2.00e-02 2.50e+03 ... (remaining 996 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 2053 2.83 - 3.35: 8482 3.35 - 3.87: 18066 3.87 - 4.38: 21277 4.38 - 4.90: 29320 Nonbonded interactions: 79198 Sorted by model distance: nonbonded pdb=" OE1 GLN B 93 " pdb=" NH1 ARG B 95 " model vdw 2.316 3.120 nonbonded pdb=" NH2 ARG E 116 " pdb=" OD1 ASP E 123 " model vdw 2.376 3.120 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.406 3.040 nonbonded pdb=" OD2 ASP D 65 " pdb=" OH TYR F 98 " model vdw 2.420 3.040 nonbonded pdb=" OE1 GLU D 68 " pdb=" NZ LYS F 91 " model vdw 2.427 3.120 ... (remaining 79193 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' and resid 38 through 134) } ncs_group { reference = (chain 'B' and resid 24 through 102) selection = chain 'F' } 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: 2.420 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: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.360 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:9.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 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 : 0.005 0.082 9605 Z= 0.230 Angle : 0.911 5.999 13907 Z= 0.590 Chirality : 0.061 0.341 1579 Planarity : 0.014 0.138 999 Dihedral : 27.253 167.075 4150 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.21 % Allowed : 0.43 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.31), residues: 548 helix: 0.73 (0.23), residues: 394 sheet: None (None), residues: 0 loop : -0.05 (0.44), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.004 ARG A 83 TYR 0.027 0.004 TYR C 57 PHE 0.010 0.001 PHE F 100 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 9605) covalent geometry : angle 0.91121 (13907) hydrogen bonds : bond 0.12610 ( 591) hydrogen bonds : angle 4.54469 ( 1464) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: B 74 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7738 (mt-10) REVERT: C 90 ASP cc_start: 0.8348 (t70) cc_final: 0.8132 (t70) REVERT: F 31 LYS cc_start: 0.8916 (tttt) cc_final: 0.8648 (tttp) outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 0.9139 time to fit residues: 173.1873 Evaluate side-chains 123 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 68 GLN A 125 GLN C 73 ASN D 44 GLN D 46 HIS D 92 GLN E 68 GLN E 85 GLN E 125 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.081000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.055775 restraints weight = 24097.500| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.12 r_work: 0.2750 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9605 Z= 0.189 Angle : 0.635 5.556 13907 Z= 0.388 Chirality : 0.038 0.140 1579 Planarity : 0.005 0.044 999 Dihedral : 31.796 164.594 3019 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 4.05 % Allowed : 16.42 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.76 (0.35), residues: 548 helix: 2.44 (0.25), residues: 399 sheet: None (None), residues: 0 loop : 0.17 (0.47), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 92 TYR 0.010 0.001 TYR C 57 PHE 0.008 0.001 PHE A 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 9605) covalent geometry : angle 0.63523 (13907) hydrogen bonds : bond 0.04429 ( 591) hydrogen bonds : angle 2.99526 ( 1464) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8778 (tp30) cc_final: 0.8493 (tp30) REVERT: F 31 LYS cc_start: 0.9071 (tttt) cc_final: 0.8839 (tttp) REVERT: F 63 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8394 (mt-10) outliers start: 19 outliers final: 5 residues processed: 147 average time/residue: 0.7875 time to fit residues: 121.1757 Evaluate side-chains 130 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 125 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 73 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 55 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 61 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 45 optimal weight: 0.5980 chunk 53 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 113 HIS ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN D 44 GLN D 46 HIS E 39 HIS E 68 GLN E 125 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.079191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.054045 restraints weight = 24195.412| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.08 r_work: 0.2707 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9605 Z= 0.226 Angle : 0.607 5.460 13907 Z= 0.367 Chirality : 0.036 0.134 1579 Planarity : 0.005 0.076 999 Dihedral : 31.503 173.238 3019 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.62 % Allowed : 19.62 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.08 (0.35), residues: 548 helix: 2.69 (0.25), residues: 402 sheet: None (None), residues: 0 loop : 0.17 (0.48), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 83 TYR 0.009 0.001 TYR F 51 PHE 0.010 0.002 PHE E 78 HIS 0.005 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00508 ( 9605) covalent geometry : angle 0.60739 (13907) hydrogen bonds : bond 0.04280 ( 591) hydrogen bonds : angle 2.92616 ( 1464) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: B 35 ARG cc_start: 0.9324 (mmm-85) cc_final: 0.9107 (mmm-85) REVERT: B 53 GLU cc_start: 0.8785 (tp30) cc_final: 0.8507 (tp30) REVERT: C 56 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8488 (tt0) REVERT: D 90 GLU cc_start: 0.8670 (mp0) cc_final: 0.8051 (mp0) REVERT: F 31 LYS cc_start: 0.9113 (tttt) cc_final: 0.8864 (tttp) outliers start: 17 outliers final: 9 residues processed: 141 average time/residue: 0.7617 time to fit residues: 112.4727 Evaluate side-chains 139 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 73 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 19 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 68 GLN E 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.080451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.055358 restraints weight = 24411.341| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.10 r_work: 0.2740 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9605 Z= 0.172 Angle : 0.584 5.769 13907 Z= 0.353 Chirality : 0.034 0.127 1579 Planarity : 0.004 0.045 999 Dihedral : 31.376 176.058 3019 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.41 % Allowed : 21.32 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.25 (0.36), residues: 548 helix: 2.83 (0.26), residues: 404 sheet: None (None), residues: 0 loop : 0.15 (0.49), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 83 TYR 0.007 0.001 TYR B 51 PHE 0.017 0.001 PHE E 78 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 9605) covalent geometry : angle 0.58399 (13907) hydrogen bonds : bond 0.03682 ( 591) hydrogen bonds : angle 2.76329 ( 1464) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8757 (tp30) cc_final: 0.8534 (tp30) REVERT: C 56 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8451 (tt0) REVERT: D 90 GLU cc_start: 0.8645 (mp0) cc_final: 0.8444 (mp0) outliers start: 16 outliers final: 10 residues processed: 139 average time/residue: 0.7242 time to fit residues: 105.6611 Evaluate side-chains 136 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 49 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 41 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 125 GLN E 68 GLN E 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.078422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.052969 restraints weight = 24274.573| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.11 r_work: 0.2674 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 9605 Z= 0.269 Angle : 0.619 6.492 13907 Z= 0.368 Chirality : 0.036 0.136 1579 Planarity : 0.004 0.045 999 Dihedral : 31.559 179.082 3019 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.90 % Allowed : 20.04 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.21 (0.36), residues: 548 helix: 2.81 (0.26), residues: 404 sheet: None (None), residues: 0 loop : 0.10 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 35 TYR 0.010 0.001 TYR F 51 PHE 0.012 0.001 PHE E 78 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00608 ( 9605) covalent geometry : angle 0.61908 (13907) hydrogen bonds : bond 0.04319 ( 591) hydrogen bonds : angle 2.93235 ( 1464) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8528 (tt0) REVERT: C 64 GLU cc_start: 0.9255 (OUTLIER) cc_final: 0.8591 (tp30) REVERT: D 90 GLU cc_start: 0.8720 (mp0) cc_final: 0.8477 (mp0) REVERT: E 59 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8085 (pm20) REVERT: F 31 LYS cc_start: 0.9125 (tttt) cc_final: 0.8892 (tttp) outliers start: 23 outliers final: 11 residues processed: 139 average time/residue: 0.8038 time to fit residues: 116.9015 Evaluate side-chains 136 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 73 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 68 GLN E 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.079109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.053874 restraints weight = 24121.475| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.08 r_work: 0.2699 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9605 Z= 0.203 Angle : 0.599 7.587 13907 Z= 0.358 Chirality : 0.034 0.129 1579 Planarity : 0.004 0.047 999 Dihedral : 31.437 177.656 3019 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.26 % Allowed : 21.11 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.26 (0.36), residues: 548 helix: 2.84 (0.26), residues: 404 sheet: None (None), residues: 0 loop : 0.14 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 35 TYR 0.009 0.001 TYR F 51 PHE 0.013 0.001 PHE E 78 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 9605) covalent geometry : angle 0.59903 (13907) hydrogen bonds : bond 0.03968 ( 591) hydrogen bonds : angle 2.83934 ( 1464) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8771 (mttm) REVERT: B 53 GLU cc_start: 0.8760 (tp30) cc_final: 0.8511 (tp30) REVERT: C 56 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8514 (tt0) REVERT: C 64 GLU cc_start: 0.9251 (OUTLIER) cc_final: 0.8594 (tp30) REVERT: D 90 GLU cc_start: 0.8701 (mp0) cc_final: 0.8478 (mp0) REVERT: E 59 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8157 (pm20) outliers start: 20 outliers final: 11 residues processed: 136 average time/residue: 0.7964 time to fit residues: 113.4266 Evaluate side-chains 138 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 49 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 17 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.078784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.053741 restraints weight = 24429.183| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.07 r_work: 0.2696 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9605 Z= 0.230 Angle : 0.605 6.456 13907 Z= 0.361 Chirality : 0.034 0.128 1579 Planarity : 0.005 0.050 999 Dihedral : 31.319 175.337 3019 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.90 % Allowed : 20.47 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.27 (0.36), residues: 548 helix: 2.85 (0.26), residues: 404 sheet: None (None), residues: 0 loop : 0.14 (0.52), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 35 TYR 0.009 0.001 TYR D 80 PHE 0.012 0.001 PHE E 78 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00518 ( 9605) covalent geometry : angle 0.60489 (13907) hydrogen bonds : bond 0.04109 ( 591) hydrogen bonds : angle 2.84661 ( 1464) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: A 64 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8733 (mttm) REVERT: B 53 GLU cc_start: 0.8725 (tp30) cc_final: 0.8503 (tp30) REVERT: C 56 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8504 (tt0) REVERT: C 64 GLU cc_start: 0.9256 (OUTLIER) cc_final: 0.8583 (tp30) REVERT: D 90 GLU cc_start: 0.8701 (mp0) cc_final: 0.8497 (mp0) REVERT: E 59 GLU cc_start: 0.8819 (pm20) cc_final: 0.8464 (pm20) outliers start: 23 outliers final: 13 residues processed: 139 average time/residue: 0.7941 time to fit residues: 115.6054 Evaluate side-chains 137 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 49 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 36 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.079068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.053663 restraints weight = 24322.840| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.11 r_work: 0.2699 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9605 Z= 0.210 Angle : 0.608 8.428 13907 Z= 0.361 Chirality : 0.034 0.129 1579 Planarity : 0.004 0.045 999 Dihedral : 31.326 175.099 3019 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.48 % Allowed : 23.24 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.25 (0.36), residues: 548 helix: 2.85 (0.26), residues: 404 sheet: None (None), residues: 0 loop : 0.08 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 35 TYR 0.011 0.002 TYR D 80 PHE 0.013 0.001 PHE E 78 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 9605) covalent geometry : angle 0.60781 (13907) hydrogen bonds : bond 0.04003 ( 591) hydrogen bonds : angle 2.82691 ( 1464) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8730 (mttm) REVERT: B 53 GLU cc_start: 0.8714 (tp30) cc_final: 0.8505 (tp30) REVERT: C 56 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8510 (tt0) REVERT: C 64 GLU cc_start: 0.9258 (OUTLIER) cc_final: 0.8590 (tp30) REVERT: D 90 GLU cc_start: 0.8689 (mp0) cc_final: 0.8485 (mp0) REVERT: E 59 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8193 (pm20) outliers start: 21 outliers final: 14 residues processed: 133 average time/residue: 0.7397 time to fit residues: 103.2626 Evaluate side-chains 140 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 49 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 25 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.079386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.054134 restraints weight = 24114.981| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.07 r_work: 0.2706 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9605 Z= 0.204 Angle : 0.607 7.487 13907 Z= 0.361 Chirality : 0.034 0.128 1579 Planarity : 0.004 0.046 999 Dihedral : 31.313 174.757 3019 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.69 % Allowed : 22.81 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.26 (0.36), residues: 548 helix: 2.85 (0.25), residues: 404 sheet: None (None), residues: 0 loop : 0.11 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 35 TYR 0.014 0.001 TYR D 80 PHE 0.013 0.001 PHE E 78 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 9605) covalent geometry : angle 0.60703 (13907) hydrogen bonds : bond 0.03890 ( 591) hydrogen bonds : angle 2.82239 ( 1464) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8713 (mttm) REVERT: B 53 GLU cc_start: 0.8705 (tp30) cc_final: 0.8462 (tp30) REVERT: C 56 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8503 (tt0) REVERT: C 64 GLU cc_start: 0.9250 (OUTLIER) cc_final: 0.8579 (tp30) REVERT: D 90 GLU cc_start: 0.8678 (mp0) cc_final: 0.8474 (mp0) REVERT: E 59 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8532 (pm20) outliers start: 22 outliers final: 13 residues processed: 133 average time/residue: 0.7615 time to fit residues: 106.2158 Evaluate side-chains 140 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 49 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 68 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 108 ASN E 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.079848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.054661 restraints weight = 24116.530| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.08 r_work: 0.2720 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9605 Z= 0.173 Angle : 0.604 7.606 13907 Z= 0.359 Chirality : 0.033 0.128 1579 Planarity : 0.005 0.052 999 Dihedral : 31.317 174.555 3019 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.41 % Allowed : 23.88 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.28 (0.36), residues: 548 helix: 2.83 (0.25), residues: 405 sheet: None (None), residues: 0 loop : 0.20 (0.52), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 35 TYR 0.019 0.002 TYR F 88 PHE 0.010 0.001 PHE E 78 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 9605) covalent geometry : angle 0.60365 (13907) hydrogen bonds : bond 0.03812 ( 591) hydrogen bonds : angle 2.78285 ( 1464) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8696 (mttm) REVERT: B 53 GLU cc_start: 0.8692 (tp30) cc_final: 0.8452 (tp30) REVERT: C 56 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8493 (tt0) REVERT: C 64 GLU cc_start: 0.9247 (OUTLIER) cc_final: 0.8579 (tp30) REVERT: D 90 GLU cc_start: 0.8656 (mp0) cc_final: 0.8439 (mp0) REVERT: E 59 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8539 (pm20) outliers start: 16 outliers final: 11 residues processed: 134 average time/residue: 0.7810 time to fit residues: 109.6807 Evaluate side-chains 141 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 49 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 63 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.078732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.053415 restraints weight = 23896.268| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.08 r_work: 0.2690 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 9605 Z= 0.248 Angle : 0.619 7.224 13907 Z= 0.367 Chirality : 0.035 0.129 1579 Planarity : 0.005 0.048 999 Dihedral : 31.323 171.845 3019 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.41 % Allowed : 23.88 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.30 (0.36), residues: 548 helix: 2.85 (0.25), residues: 405 sheet: None (None), residues: 0 loop : 0.19 (0.52), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 35 TYR 0.009 0.001 TYR D 39 PHE 0.013 0.001 PHE E 78 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00561 ( 9605) covalent geometry : angle 0.61876 (13907) hydrogen bonds : bond 0.04144 ( 591) hydrogen bonds : angle 2.90255 ( 1464) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3319.93 seconds wall clock time: 57 minutes 2.12 seconds (3422.12 seconds total)