Starting phenix.real_space_refine on Fri Feb 14 17:27:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8com_16777/02_2025/8com_16777.cif Found real_map, /net/cci-nas-00/data/ceres_data/8com_16777/02_2025/8com_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_16777/02_2025/8com_16777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8com_16777/02_2025/8com_16777.map" model { file = "/net/cci-nas-00/data/ceres_data/8com_16777/02_2025/8com_16777.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8com_16777/02_2025/8com_16777.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.60, per 1000 atoms: 0.62 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: 2.61 Conformation dependent library (CDL) restraints added in 683.1 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: 5.15 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: 3.92 Time building geometry restraints manager: 3.04 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: 2.200 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: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 29.580 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.240 ------------------------------------------------------------------------------- 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= 0.204 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (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 TRP 0.007 0.001 TRP H 25 HIS 0.001 0.000 HIS D 97 PHE 0.011 0.002 PHE H 58 TYR 0.030 0.002 TYR H 28 ARG 0.004 0.000 ARG H 19 *********************** 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 : 0.754 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 79 average time/residue: 0.2301 time to fit residues: 26.0304 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 : 0.939 ------------------------------------------------------------------------------- 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 76 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.4143 r_free = 0.4143 target = 0.173359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.124630 restraints weight = 14409.040| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.83 r_work: 0.3394 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.0655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11391 Z= 0.215 Angle : 0.568 7.199 16465 Z= 0.339 Chirality : 0.033 0.129 1900 Planarity : 0.003 0.035 1198 Dihedral : 31.213 149.783 3557 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.41 % Allowed : 12.24 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.32), residues: 692 helix: 2.11 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.07 (0.46), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 25 HIS 0.001 0.000 HIS E 122 PHE 0.013 0.002 PHE E 64 TYR 0.022 0.002 TYR H 28 ARG 0.003 0.000 ARG A 46 *********************** 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 98 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.818 Fit side-chains REVERT: D 72 ASN cc_start: 0.8707 (m-40) cc_final: 0.8413 (m-40) outliers start: 14 outliers final: 11 residues processed: 93 average time/residue: 0.2366 time to fit residues: 31.2722 Evaluate side-chains 88 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 99 SER 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 86 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 75 optimal weight: 8.9990 chunk 27 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 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 = 0.4140 r_free = 0.4140 target = 0.173432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.124973 restraints weight = 14798.214| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.89 r_work: 0.3394 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11391 Z= 0.207 Angle : 0.559 9.175 16465 Z= 0.333 Chirality : 0.032 0.137 1900 Planarity : 0.003 0.042 1198 Dihedral : 31.138 149.349 3551 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.10 % Allowed : 12.41 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.32), residues: 692 helix: 2.18 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.11 (0.46), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 25 HIS 0.001 0.000 HIS E 122 PHE 0.013 0.002 PHE A 64 TYR 0.020 0.002 TYR H 28 ARG 0.003 0.000 ARG C 17 *********************** 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 103 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.782 Fit side-chains REVERT: C 39 TYR cc_start: 0.9324 (m-80) cc_final: 0.9118 (m-80) REVERT: D 72 ASN cc_start: 0.8707 (m-40) cc_final: 0.8421 (m-40) REVERT: F 90 LYS cc_start: 0.8271 (tmtt) cc_final: 0.8052 (tmtt) outliers start: 18 outliers final: 11 residues processed: 96 average time/residue: 0.2506 time to fit residues: 33.8465 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 : 0.819 ------------------------------------------------------------------------------- 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 93 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 77 THR 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 15 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4153 r_free = 0.4153 target = 0.174833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.126628 restraints weight = 14747.681| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.90 r_work: 0.3415 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11391 Z= 0.184 Angle : 0.542 7.799 16465 Z= 0.327 Chirality : 0.032 0.128 1900 Planarity : 0.003 0.046 1198 Dihedral : 30.969 148.714 3551 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.41 % Allowed : 14.31 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.32), residues: 692 helix: 2.32 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -1.12 (0.46), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 25 HIS 0.001 0.000 HIS D 97 PHE 0.013 0.002 PHE A 64 TYR 0.017 0.002 TYR H 28 ARG 0.008 0.000 ARG D 45 *********************** 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 98 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.754 Fit side-chains REVERT: B 75 ARG cc_start: 0.8796 (mmt-90) cc_final: 0.8503 (mmt90) REVERT: C 76 LYS cc_start: 0.8071 (mmtm) cc_final: 0.7289 (pttm) REVERT: D 56 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.8210 (p0) REVERT: D 72 ASN cc_start: 0.8695 (m-40) cc_final: 0.8460 (m-40) outliers start: 14 outliers final: 9 residues processed: 92 average time/residue: 0.2434 time to fit residues: 31.6357 Evaluate side-chains 88 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 D residue 93 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 55 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4157 r_free = 0.4157 target = 0.175094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.126748 restraints weight = 14782.956| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.91 r_work: 0.3418 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1525 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= 0.179 Angle : 0.538 7.994 16465 Z= 0.324 Chirality : 0.032 0.150 1900 Planarity : 0.003 0.040 1198 Dihedral : 30.939 148.272 3551 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.59 % Allowed : 14.66 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.32), residues: 692 helix: 2.37 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -1.13 (0.46), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 25 HIS 0.001 0.000 HIS D 97 PHE 0.012 0.002 PHE A 64 TYR 0.016 0.002 TYR H 28 ARG 0.002 0.000 ARG F 65 *********************** 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 100 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.743 Fit side-chains REVERT: A 76 LYS cc_start: 0.6749 (tmtt) cc_final: 0.6065 (tmtt) REVERT: B 75 ARG cc_start: 0.8786 (mmt-90) cc_final: 0.8515 (mmt90) REVERT: D 56 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.8208 (p0) REVERT: F 90 LYS cc_start: 0.8168 (tmtt) cc_final: 0.7928 (tmtt) outliers start: 15 outliers final: 10 residues processed: 93 average time/residue: 0.2635 time to fit residues: 33.6714 Evaluate side-chains 91 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 D residue 93 ASP Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain G residue 74 THR 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 86 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 49 optimal weight: 7.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.175028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.126400 restraints weight = 14935.069| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.92 r_work: 0.3411 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11391 Z= 0.188 Angle : 0.537 8.228 16465 Z= 0.324 Chirality : 0.032 0.125 1900 Planarity : 0.003 0.038 1198 Dihedral : 30.931 148.073 3551 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.79 % Allowed : 14.83 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.32), residues: 692 helix: 2.36 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -1.18 (0.46), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 25 HIS 0.001 0.000 HIS E 110 PHE 0.011 0.001 PHE A 64 TYR 0.015 0.001 TYR H 28 ARG 0.004 0.000 ARG H 75 *********************** 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 108 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.732 Fit side-chains REVERT: A 76 LYS cc_start: 0.6889 (tmtt) cc_final: 0.6259 (tmtt) REVERT: B 75 ARG cc_start: 0.8784 (mmt-90) cc_final: 0.8515 (mmt90) REVERT: D 56 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.8217 (p0) REVERT: D 72 ASN cc_start: 0.8578 (m110) cc_final: 0.8206 (m110) REVERT: F 66 ASP cc_start: 0.8315 (m-30) cc_final: 0.8105 (m-30) REVERT: F 90 LYS cc_start: 0.8245 (tmtt) cc_final: 0.7993 (tmtt) outliers start: 22 outliers final: 13 residues processed: 99 average time/residue: 0.2413 time to fit residues: 33.1422 Evaluate side-chains 98 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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 C residue 81 THR 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 106 VAL Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 74 THR 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 69 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 82 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 chunk 39 optimal weight: 0.3980 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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 = 0.4101 r_free = 0.4101 target = 0.170303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.121400 restraints weight = 15114.145| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.92 r_work: 0.3356 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11391 Z= 0.267 Angle : 0.580 8.872 16465 Z= 0.343 Chirality : 0.034 0.139 1900 Planarity : 0.003 0.034 1198 Dihedral : 31.162 150.385 3551 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.28 % Allowed : 15.34 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.32), residues: 692 helix: 2.08 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -1.27 (0.45), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 25 HIS 0.001 0.000 HIS D 97 PHE 0.015 0.002 PHE E 64 TYR 0.018 0.002 TYR H 28 ARG 0.006 0.000 ARG H 19 *********************** 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 109 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.796 Fit side-chains REVERT: B 75 ARG cc_start: 0.8851 (mmt-90) cc_final: 0.8578 (mmt90) REVERT: F 66 ASP cc_start: 0.8542 (m-30) cc_final: 0.8322 (m-30) outliers start: 19 outliers final: 16 residues processed: 99 average time/residue: 0.2500 time to fit residues: 34.4676 Evaluate side-chains 103 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 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 57 LEU Chi-restraints excluded: chain D residue 106 VAL 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 19 VAL Chi-restraints excluded: chain G residue 74 THR 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 72 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4136 r_free = 0.4136 target = 0.173537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.124845 restraints weight = 14911.860| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.91 r_work: 0.3395 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2201 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= 0.184 Angle : 0.550 8.694 16465 Z= 0.328 Chirality : 0.032 0.134 1900 Planarity : 0.003 0.036 1198 Dihedral : 30.902 150.166 3551 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.41 % Allowed : 17.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.32), residues: 692 helix: 2.24 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -1.27 (0.45), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 25 HIS 0.001 0.000 HIS E 110 PHE 0.014 0.002 PHE A 64 TYR 0.015 0.002 TYR H 28 ARG 0.009 0.000 ARG B 25 *********************** 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 98 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.791 Fit side-chains REVERT: A 76 LYS cc_start: 0.6820 (tmtt) cc_final: 0.6303 (tmtt) REVERT: B 75 ARG cc_start: 0.8778 (mmt-90) cc_final: 0.8523 (mmt90) REVERT: D 56 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.8240 (p0) outliers start: 14 outliers final: 11 residues processed: 91 average time/residue: 0.2730 time to fit residues: 34.2251 Evaluate side-chains 94 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 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 106 VAL Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 77 THR 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 40 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 0.0970 chunk 16 optimal weight: 8.9990 chunk 52 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.174501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.125950 restraints weight = 14914.833| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.92 r_work: 0.3409 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2263 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= 0.171 Angle : 0.545 7.578 16465 Z= 0.325 Chirality : 0.032 0.124 1900 Planarity : 0.003 0.036 1198 Dihedral : 30.866 149.745 3551 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.07 % Allowed : 18.79 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.32), residues: 692 helix: 2.30 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -1.23 (0.45), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 25 HIS 0.001 0.000 HIS H 97 PHE 0.015 0.002 PHE E 64 TYR 0.015 0.002 TYR H 28 ARG 0.006 0.000 ARG B 25 *********************** 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 96 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.788 Fit side-chains REVERT: A 76 LYS cc_start: 0.6813 (tmtt) cc_final: 0.6279 (tmtt) REVERT: B 75 ARG cc_start: 0.8750 (mmt-90) cc_final: 0.8513 (mmt90) REVERT: D 45 ARG cc_start: 0.7665 (tpp80) cc_final: 0.7429 (ttm-80) outliers start: 12 outliers final: 11 residues processed: 92 average time/residue: 0.2732 time to fit residues: 34.6294 Evaluate side-chains 91 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 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 74 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 43 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 25 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN B 86 ASN D 72 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.171409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.122611 restraints weight = 14907.416| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.91 r_work: 0.3367 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11391 Z= 0.248 Angle : 0.576 8.424 16465 Z= 0.337 Chirality : 0.033 0.132 1900 Planarity : 0.003 0.034 1198 Dihedral : 31.032 150.554 3551 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.59 % Allowed : 18.79 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.31), residues: 692 helix: 2.11 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.33 (0.45), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 25 HIS 0.002 0.000 HIS A 110 PHE 0.013 0.002 PHE E 64 TYR 0.015 0.002 TYR H 28 ARG 0.006 0.000 ARG B 25 ********************** 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 102 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.792 Fit side-chains REVERT: A 76 LYS cc_start: 0.6893 (tmtt) cc_final: 0.6367 (tmtt) REVERT: C 76 LYS cc_start: 0.8406 (tptt) cc_final: 0.7650 (pttm) REVERT: D 45 ARG cc_start: 0.7743 (tpp80) cc_final: 0.7478 (ttm-80) outliers start: 15 outliers final: 13 residues processed: 96 average time/residue: 0.2651 time to fit residues: 35.1499 Evaluate side-chains 98 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 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 19 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 43 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 0 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.4110 r_free = 0.4110 target = 0.171389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.122647 restraints weight = 14758.989| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.90 r_work: 0.3364 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11391 Z= 0.249 Angle : 0.574 8.290 16465 Z= 0.337 Chirality : 0.033 0.131 1900 Planarity : 0.003 0.034 1198 Dihedral : 31.007 151.314 3551 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.41 % Allowed : 18.28 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.31), residues: 692 helix: 2.10 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -1.32 (0.45), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 25 HIS 0.001 0.000 HIS E 110 PHE 0.012 0.002 PHE H 58 TYR 0.014 0.002 TYR H 28 ARG 0.006 0.000 ARG B 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4273.56 seconds wall clock time: 76 minutes 38.77 seconds (4598.77 seconds total)