Starting phenix.real_space_refine on Mon Jun 24 19:50:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yc0_39128/06_2024/8yc0_39128_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yc0_39128/06_2024/8yc0_39128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yc0_39128/06_2024/8yc0_39128.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yc0_39128/06_2024/8yc0_39128.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yc0_39128/06_2024/8yc0_39128_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yc0_39128/06_2024/8yc0_39128_updated.pdb" } resolution = 4.12 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= 0.004 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: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 3009 2.51 5 N 731 2.21 5 O 858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 59": "OD1" <-> "OD2" Residue "d GLU 98": "OE1" <-> "OE2" Residue "d ASP 100": "OD1" <-> "OD2" Residue "e ASP 63": "OD1" <-> "OD2" Residue "e PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 124": "OE1" <-> "OE2" Residue "f TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 38": "OE1" <-> "OE2" Residue "g ASP 39": "OD1" <-> "OD2" Residue "g PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 80": "OD1" <-> "OD2" Residue "n TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 4635 Number of models: 1 Model: "" Number of chains: 9 Chain: "a" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 203 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "b" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 218 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "d" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 817 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "e" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 959 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "f" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 933 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain breaks: 1 Chain: "g" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 907 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "m" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 268 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "n" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 302 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.15, per 1000 atoms: 0.68 Number of scatterers: 4635 At special positions: 0 Unit cell: (100.004, 86.96, 89.134, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 858 8.00 N 731 7.00 C 3009 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS a 32 " - pdb=" SG CYS b 32 " distance=2.03 Simple disulfide: pdb=" SG CYS d 37 " - pdb=" SG CYS d 73 " distance=2.04 Simple disulfide: pdb=" SG CYS d 93 " - pdb=" SG CYS d 96 " distance=2.03 Simple disulfide: pdb=" SG CYS e 49 " - pdb=" SG CYS e 98 " distance=2.04 Simple disulfide: pdb=" SG CYS e 119 " - pdb=" SG CYS e 122 " distance=2.03 Simple disulfide: pdb=" SG CYS f 49 " - pdb=" SG CYS f 98 " distance=2.03 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 122 " distance=2.03 Simple disulfide: pdb=" SG CYS g 46 " - pdb=" SG CYS g 87 " distance=2.03 Simple disulfide: pdb=" SG CYS g 104 " - pdb=" SG CYS g 107 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.81 Conformation dependent library (CDL) restraints added in 833.5 milliseconds 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1084 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 9 helices and 8 sheets defined 37.7% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'a' and resid 27 through 49 removed outlier: 4.222A pdb=" N LEU a 31 " --> pdb=" O LEU a 27 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR a 33 " --> pdb=" O PRO a 29 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU a 34 " --> pdb=" O LYS a 30 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU a 35 " --> pdb=" O LEU a 31 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 53 Processing helix chain 'd' and resid 101 through 125 removed outlier: 3.854A pdb=" N ALA d 105 " --> pdb=" O PRO d 101 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLY d 106 " --> pdb=" O ALA d 102 " (cutoff:3.500A) Processing helix chain 'e' and resid 127 through 151 Processing helix chain 'f' and resid 127 through 153 Processing helix chain 'g' and resid 77 through 79 No H-bonds generated for 'chain 'g' and resid 77 through 79' Processing helix chain 'g' and resid 112 through 136 removed outlier: 3.694A pdb=" N SER g 116 " --> pdb=" O ALA g 112 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLY g 117 " --> pdb=" O ALA g 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 257 through 288 removed outlier: 3.582A pdb=" N MET m 261 " --> pdb=" O GLU m 257 " (cutoff:3.500A) Processing helix chain 'n' and resid 253 through 287 Processing sheet with id= A, first strand: chain 'd' and resid 84 through 89 removed outlier: 3.934A pdb=" N GLU d 45 " --> pdb=" O ILE d 70 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG d 72 " --> pdb=" O TRP d 43 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N TRP d 43 " --> pdb=" O ARG d 72 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'd' and resid 32 through 35 removed outlier: 3.839A pdb=" N VAL d 33 " --> pdb=" O GLY d 61 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLY d 61 " --> pdb=" O VAL d 33 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL d 35 " --> pdb=" O ASP d 59 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ASP d 59 " --> pdb=" O VAL d 35 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'e' and resid 37 through 41 removed outlier: 3.705A pdb=" N LYS e 37 " --> pdb=" O THR e 48 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'e' and resid 58 through 61 removed outlier: 3.808A pdb=" N LEU e 58 " --> pdb=" O TYR e 99 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TYR e 99 " --> pdb=" O LEU e 58 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL e 97 " --> pdb=" O GLN e 60 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'f' and resid 44 through 47 removed outlier: 3.776A pdb=" N LEU f 82 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'g' and resid 31 through 34 removed outlier: 3.960A pdb=" N LEU g 43 " --> pdb=" O TYR g 34 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY g 75 " --> pdb=" O VAL g 42 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU g 44 " --> pdb=" O ASN g 73 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ASN g 73 " --> pdb=" O LEU g 44 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'g' and resid 82 through 85 removed outlier: 3.752A pdb=" N GLY g 83 " --> pdb=" O VAL g 99 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'g' and resid 54 through 57 removed outlier: 6.909A pdb=" N LYS g 57 " --> pdb=" O MET g 61 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N MET g 61 " --> pdb=" O LYS g 57 " (cutoff:3.500A) 207 hydrogen bonds defined for protein. 609 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.97 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1433 1.34 - 1.47: 1125 1.47 - 1.59: 2115 1.59 - 1.71: 0 1.71 - 1.83: 51 Bond restraints: 4724 Sorted by residual: bond pdb=" C ASP a 28 " pdb=" N PRO a 29 " ideal model delta sigma weight residual 1.333 1.364 -0.031 1.44e-02 4.82e+03 4.62e+00 bond pdb=" CA ASP e 63 " pdb=" CB ASP e 63 " ideal model delta sigma weight residual 1.530 1.551 -0.021 1.69e-02 3.50e+03 1.55e+00 bond pdb=" CB PRO f 100 " pdb=" CG PRO f 100 " ideal model delta sigma weight residual 1.492 1.552 -0.060 5.00e-02 4.00e+02 1.46e+00 bond pdb=" N ASN e 121 " pdb=" CA ASN e 121 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.17e+00 bond pdb=" CB ASP f 137 " pdb=" CG ASP f 137 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.10e+00 ... (remaining 4719 not shown) Histogram of bond angle deviations from ideal: 98.68 - 105.75: 69 105.75 - 112.82: 2565 112.82 - 119.89: 1543 119.89 - 126.96: 2189 126.96 - 134.02: 38 Bond angle restraints: 6404 Sorted by residual: angle pdb=" C LEU a 27 " pdb=" CA LEU a 27 " pdb=" CB LEU a 27 " ideal model delta sigma weight residual 115.89 109.41 6.48 1.32e+00 5.74e-01 2.41e+01 angle pdb=" CA CYS f 49 " pdb=" CB CYS f 49 " pdb=" SG CYS f 49 " ideal model delta sigma weight residual 114.40 123.14 -8.74 2.30e+00 1.89e-01 1.44e+01 angle pdb=" CA LEU f 114 " pdb=" CB LEU f 114 " pdb=" CG LEU f 114 " ideal model delta sigma weight residual 116.30 129.15 -12.85 3.50e+00 8.16e-02 1.35e+01 angle pdb=" N GLY d 46 " pdb=" CA GLY d 46 " pdb=" C GLY d 46 " ideal model delta sigma weight residual 111.56 115.25 -3.69 1.01e+00 9.80e-01 1.33e+01 angle pdb=" CB MET m 262 " pdb=" CG MET m 262 " pdb=" SD MET m 262 " ideal model delta sigma weight residual 112.70 123.09 -10.39 3.00e+00 1.11e-01 1.20e+01 ... (remaining 6399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 2343 16.69 - 33.39: 390 33.39 - 50.08: 118 50.08 - 66.78: 20 66.78 - 83.47: 6 Dihedral angle restraints: 2877 sinusoidal: 1184 harmonic: 1693 Sorted by residual: dihedral pdb=" CB CYS d 37 " pdb=" SG CYS d 37 " pdb=" SG CYS d 73 " pdb=" CB CYS d 73 " ideal model delta sinusoidal sigma weight residual 93.00 175.13 -82.13 1 1.00e+01 1.00e-02 8.28e+01 dihedral pdb=" CB CYS e 49 " pdb=" SG CYS e 49 " pdb=" SG CYS e 98 " pdb=" CB CYS e 98 " ideal model delta sinusoidal sigma weight residual -86.00 -15.84 -70.16 1 1.00e+01 1.00e-02 6.34e+01 dihedral pdb=" CB CYS g 104 " pdb=" SG CYS g 104 " pdb=" SG CYS g 107 " pdb=" CB CYS g 107 " ideal model delta sinusoidal sigma weight residual -86.00 -154.55 68.55 1 1.00e+01 1.00e-02 6.09e+01 ... (remaining 2874 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 504 0.037 - 0.074: 174 0.074 - 0.111: 55 0.111 - 0.148: 16 0.148 - 0.186: 2 Chirality restraints: 751 Sorted by residual: chirality pdb=" CA ASP e 63 " pdb=" N ASP e 63 " pdb=" C ASP e 63 " pdb=" CB ASP e 63 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.61e-01 chirality pdb=" CA ILE d 70 " pdb=" N ILE d 70 " pdb=" C ILE d 70 " pdb=" CB ILE d 70 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA ASN e 121 " pdb=" N ASN e 121 " pdb=" C ASN e 121 " pdb=" CB ASN e 121 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.43e-01 ... (remaining 748 not shown) Planarity restraints: 785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR f 99 " 0.057 5.00e-02 4.00e+02 8.59e-02 1.18e+01 pdb=" N PRO f 100 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO f 100 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO f 100 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR e 99 " 0.037 5.00e-02 4.00e+02 5.70e-02 5.19e+00 pdb=" N PRO e 100 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO e 100 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO e 100 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS f 104 " 0.020 5.00e-02 4.00e+02 3.10e-02 1.53e+00 pdb=" N PRO f 105 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO f 105 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO f 105 " 0.017 5.00e-02 4.00e+02 ... (remaining 782 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 97 2.67 - 3.23: 4552 3.23 - 3.79: 7068 3.79 - 4.34: 8448 4.34 - 4.90: 13890 Nonbonded interactions: 34055 Sorted by model distance: nonbonded pdb=" OD1 ASP e 126 " pdb=" N VAL e 127 " model vdw 2.114 2.520 nonbonded pdb=" O GLN e 92 " pdb=" OH TYR e 96 " model vdw 2.225 2.440 nonbonded pdb=" N GLU f 56 " pdb=" OE1 GLU f 56 " model vdw 2.255 2.520 nonbonded pdb=" NE2 GLN e 60 " pdb=" OD1 ASN e 65 " model vdw 2.258 2.520 nonbonded pdb=" O ILE d 24 " pdb=" OH TYR e 95 " model vdw 2.279 2.440 ... (remaining 34050 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'a' and resid 28 through 50) selection = (chain 'b' and resid 28 through 50) } ncs_group { reference = (chain 'e' and (resid 33 through 69 or resid 74 through 153)) selection = (chain 'f' and resid 33 through 153) } 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 group one per residue 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: 0.330 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: 1.760 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.530 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 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 0.060 4724 Z= 0.220 Angle : 0.774 12.853 6404 Z= 0.389 Chirality : 0.043 0.186 751 Planarity : 0.005 0.086 785 Dihedral : 17.513 83.473 1766 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 0.58 % Allowed : 39.73 % Favored : 59.69 % 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: -0.95 (0.34), residues: 565 helix: 2.06 (0.33), residues: 212 sheet: -1.22 (0.64), residues: 74 loop : -2.81 (0.30), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP d 43 HIS 0.004 0.001 HIS f 61 PHE 0.020 0.001 PHE g 118 TYR 0.016 0.001 TYR b 42 ARG 0.005 0.000 ARG d 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 153 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 71 TYR cc_start: 0.7273 (m-80) cc_final: 0.6834 (m-10) REVERT: d 90 TYR cc_start: 0.7388 (m-80) cc_final: 0.6902 (m-80) REVERT: e 36 TYR cc_start: 0.6981 (m-80) cc_final: 0.5299 (m-10) REVERT: e 46 ILE cc_start: 0.8085 (mp) cc_final: 0.7838 (mm) REVERT: e 47 LEU cc_start: 0.8296 (mt) cc_final: 0.8084 (tt) REVERT: e 49 CYS cc_start: 0.6913 (t) cc_final: 0.5597 (t) REVERT: e 85 LYS cc_start: 0.7718 (mptt) cc_final: 0.7517 (mptt) REVERT: e 91 GLU cc_start: 0.8234 (tp30) cc_final: 0.8019 (tm-30) REVERT: e 92 GLN cc_start: 0.7710 (tt0) cc_final: 0.7193 (tt0) REVERT: e 117 ARG cc_start: 0.7997 (mtp180) cc_final: 0.7622 (ttt180) REVERT: e 120 GLU cc_start: 0.8013 (pp20) cc_final: 0.7719 (pp20) REVERT: e 123 MET cc_start: 0.5173 (mtt) cc_final: 0.4753 (ptp) REVERT: g 38 GLU cc_start: 0.8295 (pm20) cc_final: 0.8071 (pm20) REVERT: g 43 LEU cc_start: 0.7667 (mt) cc_final: 0.7448 (mt) REVERT: g 80 ASP cc_start: 0.8028 (m-30) cc_final: 0.7779 (t0) REVERT: g 111 ASN cc_start: 0.7321 (m110) cc_final: 0.6954 (p0) REVERT: m 286 LYS cc_start: 0.7448 (tppt) cc_final: 0.7238 (tptt) outliers start: 3 outliers final: 0 residues processed: 154 average time/residue: 0.1887 time to fit residues: 35.3104 Evaluate side-chains 136 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 6.9990 chunk 40 optimal weight: 0.0570 chunk 22 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 27 optimal weight: 0.0000 chunk 21 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.5906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 259 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6374 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 : 0.004 0.037 4724 Z= 0.257 Angle : 0.688 6.012 6404 Z= 0.357 Chirality : 0.044 0.172 751 Planarity : 0.005 0.056 785 Dihedral : 5.022 49.680 692 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.19 % Allowed : 4.26 % Favored : 95.54 % 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: -1.00 (0.34), residues: 565 helix: 2.15 (0.32), residues: 215 sheet: -1.70 (0.55), residues: 95 loop : -2.91 (0.30), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP e 59 HIS 0.008 0.002 HIS f 61 PHE 0.023 0.002 PHE b 40 TYR 0.011 0.002 TYR d 79 ARG 0.004 0.001 ARG d 57 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 71 TYR cc_start: 0.6939 (m-80) cc_final: 0.6562 (m-10) REVERT: d 87 GLN cc_start: 0.7808 (tm-30) cc_final: 0.7187 (tm-30) REVERT: e 36 TYR cc_start: 0.6984 (m-80) cc_final: 0.5845 (m-10) REVERT: e 49 CYS cc_start: 0.7256 (t) cc_final: 0.6642 (t) REVERT: e 85 LYS cc_start: 0.7602 (mppt) cc_final: 0.7373 (mptt) REVERT: e 92 GLN cc_start: 0.7823 (tt0) cc_final: 0.7527 (tt0) REVERT: e 98 CYS cc_start: 0.4241 (p) cc_final: 0.3976 (p) REVERT: e 117 ARG cc_start: 0.7724 (mtp180) cc_final: 0.7445 (ttt180) REVERT: e 120 GLU cc_start: 0.7895 (pp20) cc_final: 0.7673 (pp20) REVERT: f 106 GLU cc_start: 0.7948 (tt0) cc_final: 0.7745 (tt0) REVERT: f 115 ARG cc_start: 0.7677 (ttt180) cc_final: 0.7354 (ttt-90) REVERT: f 120 GLU cc_start: 0.8944 (tt0) cc_final: 0.8489 (tm-30) REVERT: f 121 ASN cc_start: 0.7788 (m-40) cc_final: 0.6717 (m-40) REVERT: f 128 MET cc_start: 0.6130 (mpp) cc_final: 0.5684 (mmt) REVERT: g 39 ASP cc_start: 0.9228 (p0) cc_final: 0.8958 (p0) REVERT: g 95 LYS cc_start: 0.8364 (mtpt) cc_final: 0.8053 (mtpp) REVERT: g 111 ASN cc_start: 0.7994 (m110) cc_final: 0.7442 (p0) REVERT: g 125 SER cc_start: 0.8809 (t) cc_final: 0.8519 (t) REVERT: m 284 THR cc_start: 0.9198 (m) cc_final: 0.8948 (m) REVERT: m 286 LYS cc_start: 0.7514 (tppt) cc_final: 0.7264 (tptt) REVERT: n 259 ASN cc_start: 0.7466 (OUTLIER) cc_final: 0.7055 (t0) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.1912 time to fit residues: 37.3857 Evaluate side-chains 135 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 40 optimal weight: 0.0770 chunk 33 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 0.0770 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 259 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6359 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4724 Z= 0.177 Angle : 0.626 7.459 6404 Z= 0.319 Chirality : 0.042 0.175 751 Planarity : 0.004 0.056 785 Dihedral : 4.908 51.587 692 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.34), residues: 565 helix: 2.45 (0.32), residues: 212 sheet: -1.08 (0.68), residues: 71 loop : -2.86 (0.29), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP g 55 HIS 0.003 0.001 HIS f 61 PHE 0.027 0.001 PHE b 40 TYR 0.018 0.001 TYR e 99 ARG 0.006 0.001 ARG g 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 87 GLN cc_start: 0.7442 (tm-30) cc_final: 0.6868 (tm-30) REVERT: e 49 CYS cc_start: 0.7643 (t) cc_final: 0.7115 (t) REVERT: e 98 CYS cc_start: 0.5022 (p) cc_final: 0.4233 (p) REVERT: e 117 ARG cc_start: 0.7967 (mtp180) cc_final: 0.7565 (ttt180) REVERT: f 106 GLU cc_start: 0.7918 (tt0) cc_final: 0.7533 (tt0) REVERT: f 115 ARG cc_start: 0.7728 (ttt180) cc_final: 0.7069 (tpt-90) REVERT: f 120 GLU cc_start: 0.8920 (tt0) cc_final: 0.8636 (tm-30) REVERT: f 124 GLU cc_start: 0.8440 (tt0) cc_final: 0.8144 (tp30) REVERT: f 128 MET cc_start: 0.6112 (mpp) cc_final: 0.5443 (mmt) REVERT: g 39 ASP cc_start: 0.9240 (p0) cc_final: 0.8895 (p0) REVERT: g 79 LYS cc_start: 0.8696 (mtmt) cc_final: 0.8178 (mtmt) REVERT: g 111 ASN cc_start: 0.7969 (m110) cc_final: 0.7407 (p0) REVERT: g 118 PHE cc_start: 0.8065 (t80) cc_final: 0.7793 (t80) REVERT: m 284 THR cc_start: 0.9159 (m) cc_final: 0.8906 (m) REVERT: m 286 LYS cc_start: 0.7462 (tppt) cc_final: 0.7247 (tptt) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.1769 time to fit residues: 33.3348 Evaluate side-chains 128 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 43 optimal weight: 0.0970 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 92 GLN ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4724 Z= 0.219 Angle : 0.637 6.805 6404 Z= 0.330 Chirality : 0.043 0.176 751 Planarity : 0.004 0.050 785 Dihedral : 4.876 47.097 692 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.34), residues: 565 helix: 2.29 (0.32), residues: 215 sheet: -1.05 (0.67), residues: 71 loop : -2.82 (0.29), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP f 59 HIS 0.005 0.002 HIS f 61 PHE 0.024 0.001 PHE b 40 TYR 0.010 0.001 TYR e 99 ARG 0.005 0.001 ARG g 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 70 ILE cc_start: 0.8291 (mt) cc_final: 0.7698 (tt) REVERT: d 87 GLN cc_start: 0.7566 (tm-30) cc_final: 0.7178 (tm-30) REVERT: e 49 CYS cc_start: 0.7336 (t) cc_final: 0.6518 (t) REVERT: e 92 GLN cc_start: 0.7537 (pt0) cc_final: 0.7305 (pt0) REVERT: e 98 CYS cc_start: 0.4798 (p) cc_final: 0.4106 (p) REVERT: e 115 ARG cc_start: 0.7969 (ttm-80) cc_final: 0.7564 (ttm-80) REVERT: e 117 ARG cc_start: 0.8018 (mtp180) cc_final: 0.7749 (ttt180) REVERT: f 89 GLU cc_start: 0.7964 (tt0) cc_final: 0.7210 (tt0) REVERT: f 106 GLU cc_start: 0.7926 (tt0) cc_final: 0.7586 (tt0) REVERT: f 115 ARG cc_start: 0.7784 (ttt180) cc_final: 0.7127 (tpt-90) REVERT: f 120 GLU cc_start: 0.8959 (tt0) cc_final: 0.8639 (tm-30) REVERT: f 124 GLU cc_start: 0.8428 (tt0) cc_final: 0.8037 (tp30) REVERT: f 128 MET cc_start: 0.6223 (mpp) cc_final: 0.5540 (mmt) REVERT: g 34 TYR cc_start: 0.7521 (t80) cc_final: 0.7309 (t80) REVERT: g 39 ASP cc_start: 0.9247 (p0) cc_final: 0.8872 (p0) REVERT: g 79 LYS cc_start: 0.8681 (mtmt) cc_final: 0.8479 (mtmt) REVERT: g 80 ASP cc_start: 0.8212 (t0) cc_final: 0.7435 (t0) REVERT: g 82 ARG cc_start: 0.8380 (ptp-170) cc_final: 0.7786 (ptp90) REVERT: g 95 LYS cc_start: 0.8366 (mtpt) cc_final: 0.8106 (mtpp) REVERT: g 111 ASN cc_start: 0.7863 (m110) cc_final: 0.7332 (p0) REVERT: g 118 PHE cc_start: 0.8152 (t80) cc_final: 0.7860 (t80) REVERT: m 267 LEU cc_start: 0.7974 (tt) cc_final: 0.7686 (tp) REVERT: m 286 LYS cc_start: 0.7547 (tppt) cc_final: 0.7284 (tptt) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1816 time to fit residues: 33.0179 Evaluate side-chains 129 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 17 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN e 92 GLN ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 HIS ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 259 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6398 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4724 Z= 0.187 Angle : 0.627 6.863 6404 Z= 0.320 Chirality : 0.042 0.194 751 Planarity : 0.004 0.038 785 Dihedral : 4.901 50.718 692 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.34), residues: 565 helix: 2.44 (0.33), residues: 213 sheet: -1.04 (0.62), residues: 78 loop : -2.75 (0.30), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP f 59 HIS 0.003 0.001 HIS d 89 PHE 0.024 0.001 PHE b 40 TYR 0.007 0.001 TYR d 79 ARG 0.005 0.001 ARG f 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 70 ILE cc_start: 0.8251 (mt) cc_final: 0.7764 (tt) REVERT: d 87 GLN cc_start: 0.7528 (tm-30) cc_final: 0.7235 (tm-30) REVERT: e 36 TYR cc_start: 0.6141 (m-80) cc_final: 0.5361 (m-10) REVERT: e 117 ARG cc_start: 0.7975 (mtp180) cc_final: 0.7723 (ttt180) REVERT: f 46 ILE cc_start: 0.8303 (mm) cc_final: 0.8080 (mm) REVERT: f 106 GLU cc_start: 0.7896 (tt0) cc_final: 0.7547 (tt0) REVERT: f 115 ARG cc_start: 0.7732 (ttt180) cc_final: 0.6898 (tpt-90) REVERT: f 120 GLU cc_start: 0.8975 (tt0) cc_final: 0.8585 (tm-30) REVERT: f 124 GLU cc_start: 0.8385 (tt0) cc_final: 0.8029 (tp30) REVERT: f 128 MET cc_start: 0.6214 (mpp) cc_final: 0.5529 (mmt) REVERT: g 39 ASP cc_start: 0.9246 (p0) cc_final: 0.8856 (p0) REVERT: g 43 LEU cc_start: 0.7844 (mp) cc_final: 0.7590 (mt) REVERT: g 80 ASP cc_start: 0.8089 (t0) cc_final: 0.7158 (t0) REVERT: g 82 ARG cc_start: 0.8376 (ptp-170) cc_final: 0.7814 (ptp-170) REVERT: g 111 ASN cc_start: 0.7859 (m110) cc_final: 0.7324 (p0) REVERT: g 118 PHE cc_start: 0.8221 (t80) cc_final: 0.7918 (t80) REVERT: m 267 LEU cc_start: 0.7930 (tt) cc_final: 0.7699 (tp) REVERT: m 286 LYS cc_start: 0.7544 (tppt) cc_final: 0.7299 (tptt) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.1802 time to fit residues: 33.4734 Evaluate side-chains 127 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 92 GLN ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 HIS ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6385 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4724 Z= 0.186 Angle : 0.624 6.768 6404 Z= 0.317 Chirality : 0.043 0.187 751 Planarity : 0.004 0.043 785 Dihedral : 4.897 49.183 692 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.34), residues: 565 helix: 2.42 (0.33), residues: 215 sheet: -1.05 (0.62), residues: 78 loop : -2.68 (0.31), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP f 59 HIS 0.004 0.001 HIS d 89 PHE 0.007 0.001 PHE f 110 TYR 0.007 0.001 TYR d 79 ARG 0.004 0.001 ARG d 91 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 70 ILE cc_start: 0.8237 (mt) cc_final: 0.7764 (tt) REVERT: e 98 CYS cc_start: 0.5378 (p) cc_final: 0.5176 (p) REVERT: f 46 ILE cc_start: 0.8229 (mm) cc_final: 0.7976 (mm) REVERT: f 89 GLU cc_start: 0.8064 (tt0) cc_final: 0.6995 (tt0) REVERT: f 101 ARG cc_start: 0.7997 (mtp85) cc_final: 0.7616 (mmp80) REVERT: f 106 GLU cc_start: 0.7835 (tt0) cc_final: 0.7585 (tt0) REVERT: f 115 ARG cc_start: 0.7753 (ttt180) cc_final: 0.6888 (tpt-90) REVERT: f 120 GLU cc_start: 0.8975 (tt0) cc_final: 0.8577 (tm-30) REVERT: f 124 GLU cc_start: 0.8357 (tt0) cc_final: 0.8016 (tp30) REVERT: f 128 MET cc_start: 0.6215 (mpp) cc_final: 0.5534 (mmt) REVERT: g 39 ASP cc_start: 0.9074 (p0) cc_final: 0.8730 (p0) REVERT: g 43 LEU cc_start: 0.7859 (mp) cc_final: 0.7561 (mt) REVERT: g 61 MET cc_start: 0.2187 (tpt) cc_final: 0.1640 (tpt) REVERT: g 79 LYS cc_start: 0.8535 (mtmt) cc_final: 0.8160 (mtmt) REVERT: g 80 ASP cc_start: 0.7920 (t0) cc_final: 0.6807 (t0) REVERT: g 82 ARG cc_start: 0.8339 (ptp-170) cc_final: 0.7702 (ptp-170) REVERT: g 111 ASN cc_start: 0.7852 (m110) cc_final: 0.7337 (p0) REVERT: g 118 PHE cc_start: 0.8287 (t80) cc_final: 0.7940 (t80) REVERT: m 267 LEU cc_start: 0.7921 (tt) cc_final: 0.7613 (tp) REVERT: m 284 THR cc_start: 0.9048 (m) cc_final: 0.8781 (m) REVERT: m 286 LYS cc_start: 0.7442 (tppt) cc_final: 0.7231 (tptt) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.1733 time to fit residues: 31.0568 Evaluate side-chains 123 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 52 optimal weight: 0.4980 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 92 GLN ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 HIS ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4724 Z= 0.174 Angle : 0.628 6.850 6404 Z= 0.319 Chirality : 0.043 0.190 751 Planarity : 0.004 0.043 785 Dihedral : 4.871 49.436 692 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.35), residues: 565 helix: 2.43 (0.33), residues: 215 sheet: -0.97 (0.62), residues: 78 loop : -2.67 (0.31), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP f 59 HIS 0.003 0.001 HIS d 89 PHE 0.014 0.001 PHE b 40 TYR 0.006 0.001 TYR d 79 ARG 0.003 0.000 ARG d 91 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 36 ASP cc_start: 0.8585 (t70) cc_final: 0.8268 (t70) REVERT: d 68 ARG cc_start: 0.7390 (mtp-110) cc_final: 0.6980 (mtp-110) REVERT: d 70 ILE cc_start: 0.8250 (mt) cc_final: 0.7794 (tt) REVERT: e 49 CYS cc_start: 0.7253 (t) cc_final: 0.6207 (t) REVERT: e 98 CYS cc_start: 0.4829 (p) cc_final: 0.4262 (p) REVERT: f 46 ILE cc_start: 0.8179 (mm) cc_final: 0.7956 (mm) REVERT: f 86 GLU cc_start: 0.6345 (pt0) cc_final: 0.6030 (tm-30) REVERT: f 106 GLU cc_start: 0.7919 (tt0) cc_final: 0.7623 (tt0) REVERT: f 115 ARG cc_start: 0.7692 (ttt180) cc_final: 0.6854 (tpt-90) REVERT: f 120 GLU cc_start: 0.8984 (tt0) cc_final: 0.8621 (tm-30) REVERT: f 124 GLU cc_start: 0.8355 (tt0) cc_final: 0.7991 (tp30) REVERT: f 128 MET cc_start: 0.6202 (mpp) cc_final: 0.5532 (mmt) REVERT: g 34 TYR cc_start: 0.7475 (t80) cc_final: 0.7177 (t80) REVERT: g 39 ASP cc_start: 0.9026 (p0) cc_final: 0.8697 (p0) REVERT: g 43 LEU cc_start: 0.7813 (mp) cc_final: 0.7590 (mt) REVERT: g 61 MET cc_start: 0.2157 (tpt) cc_final: 0.1398 (tpt) REVERT: g 80 ASP cc_start: 0.7939 (t0) cc_final: 0.7162 (t0) REVERT: g 82 ARG cc_start: 0.8554 (ptp-170) cc_final: 0.7955 (ptp-170) REVERT: g 109 GLU cc_start: 0.7109 (tt0) cc_final: 0.6712 (tt0) REVERT: g 111 ASN cc_start: 0.7807 (m110) cc_final: 0.7404 (p0) REVERT: m 267 LEU cc_start: 0.7862 (tt) cc_final: 0.7565 (tp) REVERT: m 284 THR cc_start: 0.9048 (m) cc_final: 0.8784 (m) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1772 time to fit residues: 31.4760 Evaluate side-chains 120 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 45 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN e 92 GLN ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 HIS ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6411 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4724 Z= 0.198 Angle : 0.664 7.872 6404 Z= 0.338 Chirality : 0.043 0.189 751 Planarity : 0.004 0.039 785 Dihedral : 4.947 47.882 692 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.35), residues: 565 helix: 2.37 (0.33), residues: 215 sheet: -1.14 (0.59), residues: 90 loop : -2.47 (0.31), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP g 72 HIS 0.004 0.001 HIS f 61 PHE 0.028 0.001 PHE g 118 TYR 0.008 0.001 TYR n 266 ARG 0.003 0.000 ARG d 91 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 68 ARG cc_start: 0.7602 (mtp-110) cc_final: 0.6921 (mtp-110) REVERT: e 36 TYR cc_start: 0.6319 (m-80) cc_final: 0.4639 (m-80) REVERT: e 49 CYS cc_start: 0.7231 (t) cc_final: 0.6171 (t) REVERT: e 98 CYS cc_start: 0.4927 (p) cc_final: 0.4323 (p) REVERT: e 112 LEU cc_start: 0.6900 (tp) cc_final: 0.6580 (tp) REVERT: f 46 ILE cc_start: 0.8126 (mm) cc_final: 0.7864 (mm) REVERT: f 86 GLU cc_start: 0.6492 (pt0) cc_final: 0.6178 (tm-30) REVERT: f 106 GLU cc_start: 0.7899 (tt0) cc_final: 0.7619 (tt0) REVERT: f 115 ARG cc_start: 0.7533 (ttt180) cc_final: 0.6840 (tpt-90) REVERT: f 124 GLU cc_start: 0.8370 (tt0) cc_final: 0.7994 (tp30) REVERT: f 128 MET cc_start: 0.6414 (mpp) cc_final: 0.5756 (mmt) REVERT: g 34 TYR cc_start: 0.7451 (t80) cc_final: 0.7191 (t80) REVERT: g 39 ASP cc_start: 0.8972 (p0) cc_final: 0.8637 (p0) REVERT: g 80 ASP cc_start: 0.7811 (t0) cc_final: 0.7582 (t0) REVERT: g 109 GLU cc_start: 0.7286 (tt0) cc_final: 0.6854 (tt0) REVERT: g 111 ASN cc_start: 0.7885 (m110) cc_final: 0.7424 (p0) REVERT: m 267 LEU cc_start: 0.7901 (tt) cc_final: 0.7562 (tp) REVERT: m 284 THR cc_start: 0.9046 (m) cc_final: 0.8749 (m) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.1577 time to fit residues: 28.8248 Evaluate side-chains 121 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 31 optimal weight: 0.0770 chunk 51 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN e 92 GLN ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 HIS ** n 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4724 Z= 0.185 Angle : 0.663 12.280 6404 Z= 0.333 Chirality : 0.043 0.220 751 Planarity : 0.004 0.049 785 Dihedral : 4.983 49.006 692 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.35), residues: 565 helix: 2.42 (0.33), residues: 215 sheet: -1.04 (0.60), residues: 85 loop : -2.55 (0.31), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP f 59 HIS 0.003 0.001 HIS f 61 PHE 0.007 0.001 PHE f 87 TYR 0.008 0.001 TYR g 85 ARG 0.009 0.001 ARG d 91 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 68 ARG cc_start: 0.7612 (mtp-110) cc_final: 0.6760 (mtp-110) REVERT: e 36 TYR cc_start: 0.6287 (m-80) cc_final: 0.4643 (m-80) REVERT: e 49 CYS cc_start: 0.7264 (t) cc_final: 0.6223 (t) REVERT: e 98 CYS cc_start: 0.5059 (p) cc_final: 0.4481 (p) REVERT: e 112 LEU cc_start: 0.6890 (tp) cc_final: 0.6594 (tp) REVERT: e 115 ARG cc_start: 0.7674 (ttm-80) cc_final: 0.7472 (ttm-80) REVERT: f 46 ILE cc_start: 0.8110 (mm) cc_final: 0.7804 (mm) REVERT: f 81 HIS cc_start: 0.6441 (t-170) cc_final: 0.6219 (t70) REVERT: f 86 GLU cc_start: 0.6485 (pt0) cc_final: 0.6135 (tm-30) REVERT: f 106 GLU cc_start: 0.7897 (tt0) cc_final: 0.7579 (tt0) REVERT: f 115 ARG cc_start: 0.7656 (ttt180) cc_final: 0.6954 (tpt-90) REVERT: f 124 GLU cc_start: 0.8351 (tt0) cc_final: 0.7985 (tp30) REVERT: f 128 MET cc_start: 0.6384 (mpp) cc_final: 0.5742 (mmt) REVERT: g 34 TYR cc_start: 0.7466 (t80) cc_final: 0.7168 (t80) REVERT: g 39 ASP cc_start: 0.8941 (p0) cc_final: 0.8608 (p0) REVERT: g 79 LYS cc_start: 0.8889 (mtmt) cc_final: 0.8460 (mtmt) REVERT: g 95 LYS cc_start: 0.8121 (mtpt) cc_final: 0.7868 (ttmt) REVERT: g 109 GLU cc_start: 0.7193 (tt0) cc_final: 0.6908 (tt0) REVERT: g 111 ASN cc_start: 0.7905 (m110) cc_final: 0.7505 (p0) REVERT: m 267 LEU cc_start: 0.7827 (tt) cc_final: 0.7516 (tp) REVERT: m 284 THR cc_start: 0.8996 (m) cc_final: 0.8739 (m) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1661 time to fit residues: 29.4968 Evaluate side-chains 119 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 26 optimal weight: 0.0000 chunk 34 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 0.0970 chunk 17 optimal weight: 7.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN e 92 GLN ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4724 Z= 0.180 Angle : 0.659 9.992 6404 Z= 0.332 Chirality : 0.043 0.166 751 Planarity : 0.004 0.039 785 Dihedral : 4.966 48.944 692 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.34), residues: 565 helix: 2.34 (0.32), residues: 215 sheet: -1.26 (0.58), residues: 91 loop : -2.72 (0.31), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP f 59 HIS 0.003 0.001 HIS f 61 PHE 0.017 0.001 PHE b 40 TYR 0.008 0.001 TYR d 79 ARG 0.005 0.001 ARG d 91 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 68 ARG cc_start: 0.7609 (mtp-110) cc_final: 0.6970 (mtp-110) REVERT: e 36 TYR cc_start: 0.6329 (m-80) cc_final: 0.4671 (m-80) REVERT: e 49 CYS cc_start: 0.7283 (t) cc_final: 0.6232 (t) REVERT: e 91 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7513 (tm-30) REVERT: e 98 CYS cc_start: 0.5215 (p) cc_final: 0.4661 (p) REVERT: e 112 LEU cc_start: 0.6953 (tp) cc_final: 0.6627 (tp) REVERT: f 46 ILE cc_start: 0.8028 (mm) cc_final: 0.7660 (mm) REVERT: f 81 HIS cc_start: 0.6358 (t-170) cc_final: 0.6113 (t70) REVERT: f 86 GLU cc_start: 0.6496 (pt0) cc_final: 0.6162 (tm-30) REVERT: f 106 GLU cc_start: 0.7890 (tt0) cc_final: 0.7562 (tt0) REVERT: f 115 ARG cc_start: 0.7491 (ttt180) cc_final: 0.7036 (tpt-90) REVERT: f 124 GLU cc_start: 0.8294 (tt0) cc_final: 0.7996 (tp30) REVERT: f 128 MET cc_start: 0.6346 (mpp) cc_final: 0.5722 (mmt) REVERT: g 34 TYR cc_start: 0.7433 (t80) cc_final: 0.7082 (t80) REVERT: g 39 ASP cc_start: 0.8928 (p0) cc_final: 0.8578 (p0) REVERT: g 79 LYS cc_start: 0.8847 (mtmt) cc_final: 0.8494 (mtmt) REVERT: g 80 ASP cc_start: 0.8133 (t70) cc_final: 0.7867 (t0) REVERT: g 82 ARG cc_start: 0.8583 (ptp-170) cc_final: 0.7912 (ptp-170) REVERT: g 95 LYS cc_start: 0.8144 (mtpt) cc_final: 0.7808 (ttmt) REVERT: g 109 GLU cc_start: 0.7174 (tt0) cc_final: 0.6855 (tt0) REVERT: g 111 ASN cc_start: 0.7891 (m110) cc_final: 0.7507 (p0) REVERT: m 267 LEU cc_start: 0.7871 (tt) cc_final: 0.7612 (tp) REVERT: m 284 THR cc_start: 0.8995 (m) cc_final: 0.8722 (m) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1601 time to fit residues: 28.8334 Evaluate side-chains 121 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN e 92 GLN n 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.168101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.148928 restraints weight = 7821.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.148313 restraints weight = 7166.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.148966 restraints weight = 7287.157| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4724 Z= 0.190 Angle : 0.661 7.038 6404 Z= 0.334 Chirality : 0.043 0.167 751 Planarity : 0.004 0.039 785 Dihedral : 4.990 48.829 692 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.34), residues: 565 helix: 2.36 (0.33), residues: 215 sheet: -1.36 (0.56), residues: 96 loop : -2.63 (0.31), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP f 59 HIS 0.002 0.001 HIS f 61 PHE 0.016 0.001 PHE b 40 TYR 0.011 0.001 TYR d 79 ARG 0.004 0.001 ARG d 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1319.87 seconds wall clock time: 24 minutes 12.31 seconds (1452.31 seconds total)