Starting phenix.real_space_refine on Wed Mar 4 03:23:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8com_16777/03_2026/8com_16777.cif Found real_map, /net/cci-nas-00/data/ceres_data/8com_16777/03_2026/8com_16777.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/cci-nas-00/data/ceres_data/8com_16777/03_2026/8com_16777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8com_16777/03_2026/8com_16777.map" model { file = "/net/cci-nas-00/data/ceres_data/8com_16777/03_2026/8com_16777.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8com_16777/03_2026/8com_16777.cif" } resolution = 3.3 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= 0.001 sd= 0.076 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 254 5.49 5 S 18 5.16 5 C 5887 2.51 5 N 2043 2.21 5 O 2503 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s 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: 10705 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 710 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "B" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 597 Classifications: {'peptide': 76} Link IDs: {'TRANS': 75} Chain: "C" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 732 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "D" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "E" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 669 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "F" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 592 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain: "G" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 736 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "I" Number of atoms: 2620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 2620 Classifications: {'DNA': 127} Link IDs: {'rna3p': 126} Chain: "J" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 2587 Classifications: {'DNA': 127} Link IDs: {'rna3p': 126} Time building chain proxies: 2.48, per 1000 atoms: 0.23 Number of scatterers: 10705 At special positions: 0 Unit cell: (73.781, 116.06, 115.231, 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 18 16.00 P 254 15.00 O 2503 8.00 N 2043 7.00 C 5887 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 388.4 milliseconds 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1316 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 9 sheets defined 74.6% alpha, 2.5% beta 126 base pairs and 210 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 42 through 53 removed outlier: 3.648A pdb=" N ARG A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 74 removed outlier: 3.589A pdb=" N ALA A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 111 removed outlier: 3.651A pdb=" N LEU A 87 " --> pdb=" O SER A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 129 Processing helix chain 'B' and resid 28 through 40 Processing helix chain 'B' and resid 47 through 74 removed outlier: 3.639A pdb=" N GLU B 51 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA B 69 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR B 70 " --> pdb=" O ASP B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 91 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 27 through 38 Processing helix chain 'C' and resid 44 through 72 removed outlier: 3.629A pdb=" N ALA C 48 " --> pdb=" O GLY C 44 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN C 72 " --> pdb=" O LYS C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 92 Processing helix chain 'C' and resid 93 through 99 Processing helix chain 'D' and resid 25 through 37 removed outlier: 3.624A pdb=" N ILE D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 73 Processing helix chain 'D' and resid 78 through 90 Processing helix chain 'D' and resid 91 through 111 removed outlier: 3.846A pdb=" N HIS D 97 " --> pdb=" O ASP D 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 54 Processing helix chain 'E' and resid 60 through 76 Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 92 through 111 removed outlier: 3.540A pdb=" N TYR E 96 " --> pdb=" O ALA E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 127 Processing helix chain 'F' and resid 28 through 40 Processing helix chain 'F' and resid 47 through 74 removed outlier: 3.734A pdb=" N GLU F 51 " --> pdb=" O VAL F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 92 Processing helix chain 'G' and resid 15 through 20 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 44 through 73 removed outlier: 3.603A pdb=" N ALA G 48 " --> pdb=" O GLY G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 92 Processing helix chain 'G' and resid 94 through 99 Processing helix chain 'H' and resid 25 through 37 Processing helix chain 'H' and resid 43 through 72 Processing helix chain 'H' and resid 79 through 90 Processing helix chain 'H' and resid 91 through 111 removed outlier: 3.680A pdb=" N HIS H 97 " --> pdb=" O ASP H 93 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER H 111 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 removed outlier: 7.234A pdb=" N ARG A 80 " --> pdb=" O VAL B 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 116 Processing sheet with id=AA3, first strand: chain 'B' and resid 95 through 96 Processing sheet with id=AA4, first strand: chain 'C' and resid 79 through 80 Processing sheet with id=AA5, first strand: chain 'C' and resid 103 through 104 removed outlier: 6.823A pdb=" N THR C 103 " --> pdb=" O TYR F 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 80 through 81 removed outlier: 8.289A pdb=" N ARG E 80 " --> pdb=" O VAL F 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 115 through 116 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.410A pdb=" N ARG G 42 " --> pdb=" O LEU H 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 79 through 80 385 hydrogen bonds defined for protein. 1155 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 327 hydrogen bonds 654 hydrogen bond angles 0 basepair planarities 126 basepair parallelities 210 stacking parallelities Total time for adding SS restraints: 2.06 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2175 1.33 - 1.45: 3568 1.45 - 1.57: 5110 1.57 - 1.69: 506 1.69 - 1.81: 32 Bond restraints: 11391 Sorted by residual: bond pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " ideal model delta sigma weight residual 1.523 1.546 -0.023 2.00e-02 2.50e+03 1.28e+00 bond pdb=" C3' DG I -21 " pdb=" O3' DG I -21 " ideal model delta sigma weight residual 1.422 1.455 -0.033 3.00e-02 1.11e+03 1.22e+00 bond pdb=" CA LYS C 76 " pdb=" C LYS C 76 " ideal model delta sigma weight residual 1.523 1.537 -0.014 1.34e-02 5.57e+03 1.08e+00 bond pdb=" CB GLU E 77 " pdb=" CG GLU E 77 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.04e+00 bond pdb=" C3' DT I -17 " pdb=" O3' DT I -17 " ideal model delta sigma weight residual 1.422 1.452 -0.030 3.00e-02 1.11e+03 1.03e+00 ... (remaining 11386 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 16136 1.80 - 3.60: 311 3.60 - 5.40: 13 5.40 - 7.20: 3 7.20 - 8.99: 2 Bond angle restraints: 16465 Sorted by residual: angle pdb=" N VAL C 27 " pdb=" CA VAL C 27 " pdb=" C VAL C 27 " ideal model delta sigma weight residual 113.47 108.61 4.86 1.01e+00 9.80e-01 2.31e+01 angle pdb=" CB MET H 47 " pdb=" CG MET H 47 " pdb=" SD MET H 47 " ideal model delta sigma weight residual 112.70 121.69 -8.99 3.00e+00 1.11e-01 8.99e+00 angle pdb=" CA LYS A 76 " pdb=" CB LYS A 76 " pdb=" CG LYS A 76 " ideal model delta sigma weight residual 114.10 119.84 -5.74 2.00e+00 2.50e-01 8.23e+00 angle pdb=" CA ASP H 56 " pdb=" CB ASP H 56 " pdb=" CG ASP H 56 " ideal model delta sigma weight residual 112.60 110.18 2.42 1.00e+00 1.00e+00 5.84e+00 angle pdb=" C3' DG J 9 " pdb=" C2' DG J 9 " pdb=" C1' DG J 9 " ideal model delta sigma weight residual 101.60 97.99 3.61 1.50e+00 4.44e-01 5.78e+00 ... (remaining 16460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.04: 4650 30.04 - 60.09: 1493 60.09 - 90.13: 40 90.13 - 120.18: 1 120.18 - 150.22: 4 Dihedral angle restraints: 6188 sinusoidal: 4152 harmonic: 2036 Sorted by residual: dihedral pdb=" C4' DT I -17 " pdb=" C3' DT I -17 " pdb=" O3' DT I -17 " pdb=" P DT I -16 " ideal model delta sinusoidal sigma weight residual 220.00 69.78 150.22 1 3.50e+01 8.16e-04 1.46e+01 dihedral pdb=" C4' DC J 4 " pdb=" C3' DC J 4 " pdb=" O3' DC J 4 " pdb=" P DC J 5 " ideal model delta sinusoidal sigma weight residual 220.00 75.92 144.08 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" C4' DG I -21 " pdb=" C3' DG I -21 " pdb=" O3' DG I -21 " pdb=" P DC I -20 " ideal model delta sinusoidal sigma weight residual 220.00 94.78 125.22 1 3.50e+01 8.16e-04 1.24e+01 ... (remaining 6185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1250 0.028 - 0.057: 495 0.057 - 0.085: 127 0.085 - 0.113: 23 0.113 - 0.142: 5 Chirality restraints: 1900 Sorted by residual: chirality pdb=" CG LEU E 127 " pdb=" CB LEU E 127 " pdb=" CD1 LEU E 127 " pdb=" CD2 LEU E 127 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA ILE B 44 " pdb=" N ILE B 44 " pdb=" C ILE B 44 " pdb=" CB ILE B 44 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.01e-01 chirality pdb=" CA ILE F 27 " pdb=" N ILE F 27 " pdb=" C ILE F 27 " pdb=" CB ILE F 27 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.62e-01 ... (remaining 1897 not shown) Planarity restraints: 1198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 20 " 0.023 2.00e-02 2.50e+03 1.11e-02 3.70e+00 pdb=" N9 DG I 20 " -0.029 2.00e-02 2.50e+03 pdb=" C8 DG I 20 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 20 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DG I 20 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 20 " 0.002 2.00e-02 2.50e+03 pdb=" O6 DG I 20 " 0.005 2.00e-02 2.50e+03 pdb=" N1 DG I 20 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 20 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 20 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DG I 20 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 20 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 28 " 0.012 2.00e-02 2.50e+03 1.23e-02 3.05e+00 pdb=" CG TYR H 28 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR H 28 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR H 28 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR H 28 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR H 28 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR H 28 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR H 28 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I -4 " 0.021 2.00e-02 2.50e+03 8.79e-03 2.32e+00 pdb=" N9 DG I -4 " -0.019 2.00e-02 2.50e+03 pdb=" C8 DG I -4 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG I -4 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DG I -4 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I -4 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG I -4 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DG I -4 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I -4 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG I -4 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DG I -4 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG I -4 " -0.002 2.00e-02 2.50e+03 ... (remaining 1195 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1639 2.76 - 3.30: 9909 3.30 - 3.83: 21739 3.83 - 4.37: 24091 4.37 - 4.90: 35191 Nonbonded interactions: 92569 Sorted by model distance: nonbonded pdb=" OE1 GLU E 91 " pdb=" OH TYR F 98 " model vdw 2.228 3.040 nonbonded pdb=" OG SER E 54 " pdb=" OD1 ASP E 56 " model vdw 2.275 3.040 nonbonded pdb=" OH TYR B 73 " pdb=" OE2 GLU D 81 " model vdw 2.284 3.040 nonbonded pdb=" OD2 ASP D 56 " pdb=" OH TYR F 96 " model vdw 2.291 3.040 nonbonded pdb=" N LYS E 61 " pdb=" OP1 DG I 18 " model vdw 2.308 3.120 ... (remaining 92564 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' and resid 45 through 129) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 24 through 98) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 15 through 111) } 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: 2.020 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.280 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11391 Z= 0.166 Angle : 0.571 8.994 16465 Z= 0.346 Chirality : 0.032 0.142 1900 Planarity : 0.003 0.029 1198 Dihedral : 28.543 150.219 4872 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.34 % Allowed : 13.97 % Favored : 85.69 % 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: 2.02 (0.32), residues: 692 helix: 2.12 (0.23), residues: 510 sheet: None (None), residues: 0 loop : -0.96 (0.43), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 19 TYR 0.030 0.002 TYR H 28 PHE 0.011 0.002 PHE H 58 TRP 0.007 0.001 TRP H 25 HIS 0.001 0.000 HIS D 97 Details of bonding type rmsd covalent geometry : bond 0.00364 (11391) covalent geometry : angle 0.57103 (16465) hydrogen bonds : bond 0.12100 ( 712) hydrogen bonds : angle 4.06014 ( 1809) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.216 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 79 average time/residue: 0.1044 time to fit residues: 11.8233 Evaluate side-chains 81 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain E residue 94 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.174522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.126145 restraints weight = 14801.521| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.90 r_work: 0.3408 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11391 Z= 0.156 Angle : 0.554 6.736 16465 Z= 0.333 Chirality : 0.032 0.132 1900 Planarity : 0.003 0.037 1198 Dihedral : 31.118 149.243 3557 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.90 % Allowed : 12.93 % Favored : 85.17 % 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: 2.20 (0.32), residues: 692 helix: 2.24 (0.23), residues: 523 sheet: None (None), residues: 0 loop : -1.11 (0.46), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 80 TYR 0.023 0.002 TYR H 28 PHE 0.012 0.002 PHE A 64 TRP 0.007 0.001 TRP D 25 HIS 0.001 0.000 HIS E 110 Details of bonding type rmsd covalent geometry : bond 0.00342 (11391) covalent geometry : angle 0.55410 (16465) hydrogen bonds : bond 0.03805 ( 712) hydrogen bonds : angle 2.84065 ( 1809) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.253 Fit side-chains REVERT: B 75 ARG cc_start: 0.8841 (mmt-90) cc_final: 0.8549 (mmt-90) REVERT: D 72 ASN cc_start: 0.8681 (m-40) cc_final: 0.8403 (m-40) REVERT: E 91 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7984 (mt-10) outliers start: 11 outliers final: 7 residues processed: 97 average time/residue: 0.1086 time to fit residues: 14.8959 Evaluate side-chains 86 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 86 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 56 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.174058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.125413 restraints weight = 14894.497| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.91 r_work: 0.3396 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11391 Z= 0.163 Angle : 0.553 8.471 16465 Z= 0.331 Chirality : 0.032 0.124 1900 Planarity : 0.003 0.040 1198 Dihedral : 31.040 148.609 3551 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.76 % Allowed : 13.10 % Favored : 84.14 % 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: 2.26 (0.32), residues: 692 helix: 2.25 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -1.03 (0.46), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 45 TYR 0.019 0.002 TYR H 28 PHE 0.012 0.002 PHE A 64 TRP 0.007 0.001 TRP D 25 HIS 0.002 0.000 HIS E 110 Details of bonding type rmsd covalent geometry : bond 0.00365 (11391) covalent geometry : angle 0.55292 (16465) hydrogen bonds : bond 0.03774 ( 712) hydrogen bonds : angle 2.75328 ( 1809) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.285 Fit side-chains REVERT: D 72 ASN cc_start: 0.8690 (m-40) cc_final: 0.8420 (m-40) REVERT: F 90 LYS cc_start: 0.8272 (tmtt) cc_final: 0.8066 (tmtt) outliers start: 16 outliers final: 12 residues processed: 93 average time/residue: 0.1173 time to fit residues: 15.1205 Evaluate side-chains 95 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 86 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 89 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.167700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.118858 restraints weight = 14840.340| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.83 r_work: 0.3328 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 11391 Z= 0.239 Angle : 0.618 9.284 16465 Z= 0.363 Chirality : 0.035 0.156 1900 Planarity : 0.004 0.039 1198 Dihedral : 31.416 150.924 3551 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 4.31 % Allowed : 13.10 % Favored : 82.59 % 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: 1.73 (0.31), residues: 692 helix: 1.86 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.17 (0.45), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 106 TYR 0.020 0.002 TYR H 28 PHE 0.016 0.002 PHE E 64 TRP 0.007 0.002 TRP H 25 HIS 0.002 0.000 HIS E 110 Details of bonding type rmsd covalent geometry : bond 0.00551 (11391) covalent geometry : angle 0.61823 (16465) hydrogen bonds : bond 0.04494 ( 712) hydrogen bonds : angle 3.11898 ( 1809) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.274 Fit side-chains REVERT: A 76 LYS cc_start: 0.7011 (tmtt) cc_final: 0.6442 (tmtt) REVERT: B 75 ARG cc_start: 0.8952 (mmt-90) cc_final: 0.8661 (mmt90) REVERT: C 76 LYS cc_start: 0.8399 (tptt) cc_final: 0.7663 (pttm) REVERT: D 72 ASN cc_start: 0.8769 (m-40) cc_final: 0.8533 (m-40) REVERT: F 45 SER cc_start: 0.9414 (t) cc_final: 0.8679 (m) REVERT: F 66 ASP cc_start: 0.8602 (m-30) cc_final: 0.8382 (m-30) outliers start: 25 outliers final: 20 residues processed: 98 average time/residue: 0.1223 time to fit residues: 16.2594 Evaluate side-chains 107 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 86 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 7 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 16 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.173125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.125002 restraints weight = 14949.870| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.90 r_work: 0.3390 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11391 Z= 0.151 Angle : 0.549 8.567 16465 Z= 0.330 Chirality : 0.032 0.124 1900 Planarity : 0.003 0.040 1198 Dihedral : 30.998 151.168 3551 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.59 % Allowed : 16.38 % Favored : 81.03 % 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: 2.15 (0.32), residues: 692 helix: 2.18 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -1.15 (0.45), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 19 TYR 0.017 0.002 TYR H 28 PHE 0.016 0.002 PHE A 64 TRP 0.009 0.002 TRP D 25 HIS 0.001 0.000 HIS E 110 Details of bonding type rmsd covalent geometry : bond 0.00331 (11391) covalent geometry : angle 0.54947 (16465) hydrogen bonds : bond 0.03599 ( 712) hydrogen bonds : angle 2.70225 ( 1809) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.176 Fit side-chains REVERT: A 76 LYS cc_start: 0.6832 (tmtt) cc_final: 0.6295 (tmtt) REVERT: B 75 ARG cc_start: 0.8853 (mmt-90) cc_final: 0.8605 (mmt90) REVERT: C 76 LYS cc_start: 0.8365 (tptt) cc_final: 0.7583 (pttm) REVERT: D 72 ASN cc_start: 0.8713 (m-40) cc_final: 0.8460 (m-40) outliers start: 15 outliers final: 10 residues processed: 101 average time/residue: 0.1057 time to fit residues: 14.8657 Evaluate side-chains 94 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 86 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 71 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.170837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.121976 restraints weight = 14965.752| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.93 r_work: 0.3358 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11391 Z= 0.187 Angle : 0.565 8.588 16465 Z= 0.336 Chirality : 0.033 0.146 1900 Planarity : 0.003 0.039 1198 Dihedral : 31.102 150.429 3551 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.28 % Allowed : 16.90 % Favored : 79.83 % 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: 2.04 (0.32), residues: 692 helix: 2.11 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -1.22 (0.45), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 17 TYR 0.015 0.002 TYR H 28 PHE 0.013 0.002 PHE A 64 TRP 0.006 0.001 TRP H 25 HIS 0.001 0.000 HIS E 110 Details of bonding type rmsd covalent geometry : bond 0.00428 (11391) covalent geometry : angle 0.56458 (16465) hydrogen bonds : bond 0.03888 ( 712) hydrogen bonds : angle 2.84530 ( 1809) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.238 Fit side-chains REVERT: A 76 LYS cc_start: 0.6873 (tmtt) cc_final: 0.6311 (tmtt) REVERT: B 75 ARG cc_start: 0.8850 (mmt-90) cc_final: 0.8610 (mmt90) REVERT: C 76 LYS cc_start: 0.8397 (tptt) cc_final: 0.7628 (pttm) REVERT: F 90 LYS cc_start: 0.8094 (tmtt) cc_final: 0.7883 (tmtt) outliers start: 19 outliers final: 13 residues processed: 98 average time/residue: 0.1092 time to fit residues: 14.9364 Evaluate side-chains 97 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 86 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 81 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 29 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 83 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.174924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.126332 restraints weight = 14931.747| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.93 r_work: 0.3412 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11391 Z= 0.143 Angle : 0.533 7.655 16465 Z= 0.321 Chirality : 0.032 0.136 1900 Planarity : 0.003 0.040 1198 Dihedral : 30.816 150.127 3551 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.90 % Allowed : 17.93 % Favored : 80.17 % 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: 2.34 (0.32), residues: 692 helix: 2.36 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.18 (0.45), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 45 TYR 0.014 0.002 TYR H 28 PHE 0.014 0.002 PHE A 64 TRP 0.009 0.002 TRP D 25 HIS 0.002 0.000 HIS E 110 Details of bonding type rmsd covalent geometry : bond 0.00311 (11391) covalent geometry : angle 0.53307 (16465) hydrogen bonds : bond 0.03527 ( 712) hydrogen bonds : angle 2.60890 ( 1809) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.256 Fit side-chains REVERT: A 76 LYS cc_start: 0.6833 (tmtt) cc_final: 0.6322 (tmtt) REVERT: B 75 ARG cc_start: 0.8783 (mmt-90) cc_final: 0.8552 (mmt90) REVERT: C 76 LYS cc_start: 0.8385 (tptt) cc_final: 0.7556 (pttp) REVERT: D 72 ASN cc_start: 0.8555 (m110) cc_final: 0.8317 (m-40) outliers start: 11 outliers final: 9 residues processed: 90 average time/residue: 0.1113 time to fit residues: 13.9404 Evaluate side-chains 89 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 86 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 29 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.174103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.125471 restraints weight = 14968.870| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.93 r_work: 0.3401 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11391 Z= 0.153 Angle : 0.538 7.324 16465 Z= 0.322 Chirality : 0.032 0.128 1900 Planarity : 0.003 0.037 1198 Dihedral : 30.869 149.821 3551 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.76 % Allowed : 17.41 % Favored : 79.83 % 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: 2.35 (0.32), residues: 692 helix: 2.37 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.17 (0.45), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 19 TYR 0.014 0.002 TYR H 28 PHE 0.013 0.002 PHE E 64 TRP 0.007 0.001 TRP D 25 HIS 0.001 0.000 HIS E 110 Details of bonding type rmsd covalent geometry : bond 0.00339 (11391) covalent geometry : angle 0.53760 (16465) hydrogen bonds : bond 0.03586 ( 712) hydrogen bonds : angle 2.63975 ( 1809) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.252 Fit side-chains REVERT: A 76 LYS cc_start: 0.6845 (tmtt) cc_final: 0.6325 (tmtt) REVERT: B 75 ARG cc_start: 0.8758 (mmt-90) cc_final: 0.8541 (mmt90) REVERT: C 76 LYS cc_start: 0.8397 (tptt) cc_final: 0.7576 (pttp) REVERT: D 56 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.8167 (p0) outliers start: 16 outliers final: 12 residues processed: 92 average time/residue: 0.1041 time to fit residues: 13.4550 Evaluate side-chains 94 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 86 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 74 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 71 optimal weight: 7.9990 chunk 64 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.172631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.123991 restraints weight = 14938.219| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.92 r_work: 0.3385 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11391 Z= 0.166 Angle : 0.546 7.862 16465 Z= 0.324 Chirality : 0.032 0.128 1900 Planarity : 0.003 0.036 1198 Dihedral : 30.912 150.741 3551 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.24 % Allowed : 18.10 % Favored : 79.66 % 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: 2.27 (0.32), residues: 692 helix: 2.30 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.18 (0.45), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 45 TYR 0.015 0.002 TYR H 28 PHE 0.014 0.002 PHE A 64 TRP 0.006 0.001 TRP D 25 HIS 0.001 0.000 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00373 (11391) covalent geometry : angle 0.54567 (16465) hydrogen bonds : bond 0.03689 ( 712) hydrogen bonds : angle 2.73340 ( 1809) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.262 Fit side-chains REVERT: B 75 ARG cc_start: 0.8793 (mmt-90) cc_final: 0.8562 (mmt90) REVERT: C 76 LYS cc_start: 0.8425 (tptt) cc_final: 0.7657 (pttp) outliers start: 13 outliers final: 12 residues processed: 91 average time/residue: 0.1080 time to fit residues: 13.5869 Evaluate side-chains 95 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 86 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 36 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 52 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.174156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.125508 restraints weight = 14870.147| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.92 r_work: 0.3400 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11391 Z= 0.153 Angle : 0.538 8.013 16465 Z= 0.321 Chirality : 0.032 0.126 1900 Planarity : 0.003 0.036 1198 Dihedral : 30.820 150.827 3551 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.59 % Allowed : 17.41 % Favored : 80.00 % 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: 2.38 (0.32), residues: 692 helix: 2.38 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.13 (0.45), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 45 TYR 0.014 0.002 TYR H 28 PHE 0.013 0.002 PHE A 64 TRP 0.007 0.001 TRP D 25 HIS 0.002 0.000 HIS E 110 Details of bonding type rmsd covalent geometry : bond 0.00341 (11391) covalent geometry : angle 0.53782 (16465) hydrogen bonds : bond 0.03543 ( 712) hydrogen bonds : angle 2.67307 ( 1809) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.309 Fit side-chains REVERT: A 76 LYS cc_start: 0.6838 (tmtt) cc_final: 0.6400 (tmtt) REVERT: B 75 ARG cc_start: 0.8793 (mmt-90) cc_final: 0.8574 (mmt90) REVERT: C 76 LYS cc_start: 0.8416 (tptt) cc_final: 0.7642 (pttp) REVERT: D 45 ARG cc_start: 0.7684 (tpp80) cc_final: 0.7437 (ttm-80) REVERT: D 56 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.8167 (p0) outliers start: 15 outliers final: 10 residues processed: 90 average time/residue: 0.1110 time to fit residues: 13.7772 Evaluate side-chains 92 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 86 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 78 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.173969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.125300 restraints weight = 14947.671| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.92 r_work: 0.3399 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11391 Z= 0.155 Angle : 0.538 8.000 16465 Z= 0.321 Chirality : 0.032 0.166 1900 Planarity : 0.003 0.036 1198 Dihedral : 30.822 150.824 3551 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.07 % Allowed : 18.10 % Favored : 79.83 % 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: 2.38 (0.32), residues: 692 helix: 2.38 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.15 (0.45), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 45 TYR 0.014 0.002 TYR H 28 PHE 0.013 0.002 PHE A 64 TRP 0.007 0.001 TRP D 25 HIS 0.001 0.000 HIS E 110 Details of bonding type rmsd covalent geometry : bond 0.00348 (11391) covalent geometry : angle 0.53827 (16465) hydrogen bonds : bond 0.03563 ( 712) hydrogen bonds : angle 2.66925 ( 1809) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2100.72 seconds wall clock time: 36 minutes 38.94 seconds (2198.94 seconds total)