Starting phenix.real_space_refine on Thu Mar 14 21:44:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ni2_9375/03_2024/6ni2_9375_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ni2_9375/03_2024/6ni2_9375.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ni2_9375/03_2024/6ni2_9375.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ni2_9375/03_2024/6ni2_9375.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ni2_9375/03_2024/6ni2_9375_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ni2_9375/03_2024/6ni2_9375_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4506 atoms to isotropic. 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 6 5.49 5 S 21 5.16 5 C 3402 2.51 5 N 910 2.21 5 O 1042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 25": "NH1" <-> "NH2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B ARG 165": "NH1" <-> "NH2" Residue "B ARG 236": "NH1" <-> "NH2" Residue "H PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 101": "NH1" <-> "NH2" Residue "L TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5381 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 865 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain: "B" Number of atoms: 2699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2699 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 72 Chain: "H" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 113} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 800 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "V" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 109 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'TPO:plan-1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 3.47, per 1000 atoms: 0.64 Number of scatterers: 5381 At special positions: 0 Unit cell: (95.68, 91.52, 109.2, 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 21 16.00 P 6 15.00 O 1042 8.00 N 910 7.00 C 3402 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.04 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.05 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.89 Conformation dependent library (CDL) restraints added in 968.1 milliseconds 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1312 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 3 helices and 14 sheets defined 2.3% alpha, 33.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'H' and resid 91 through 93 No H-bonds generated for 'chain 'H' and resid 91 through 93' Processing sheet with id= A, first strand: chain 'A' and resid 17 through 23 removed outlier: 3.728A pdb=" N MET A 82 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER A 70 " --> pdb=" O TYR A 79 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 9 through 12 Processing sheet with id= C, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.753A pdb=" N ARG B 169 " --> pdb=" O PHE B 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 74 through 78 removed outlier: 3.572A pdb=" N PHE B 75 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR B 144 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE B 168 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL B 164 " --> pdb=" O ALA B 148 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 127 through 129 Processing sheet with id= F, first strand: chain 'B' and resid 183 through 188 removed outlier: 3.680A pdb=" N HIS B 198 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 274 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR B 272 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL B 218 " --> pdb=" O LYS B 270 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS B 270 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 220 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE B 268 " --> pdb=" O VAL B 220 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 346 through 349 removed outlier: 4.629A pdb=" N TYR B 321 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS B 230 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA B 254 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLN B 237 " --> pdb=" O PRO B 252 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N ALA B 239 " --> pdb=" O LYS B 250 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LYS B 250 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ILE B 241 " --> pdb=" O GLN B 248 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLN B 248 " --> pdb=" O ILE B 241 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 53 through 59 removed outlier: 3.810A pdb=" N PHE B 87 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL B 55 " --> pdb=" O GLN B 85 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N GLN B 85 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU B 57 " --> pdb=" O ASN B 83 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ASN B 83 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N CYS B 59 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N VAL B 81 " --> pdb=" O CYS B 59 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.557A pdb=" N SER H 24 " --> pdb=" O SER H 10 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU H 21 " --> pdb=" O MET H 86 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 117 through 119 removed outlier: 6.349A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 100 through 102 removed outlier: 4.257A pdb=" N TYR H 112 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 5 through 8 Processing sheet with id= M, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.272A pdb=" N LYS L 104 " --> pdb=" O LEU L 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'L' and resid 86 through 91 removed outlier: 5.847A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) 140 hydrogen bonds defined for protein. 375 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: 1.30 Time building geometry restraints manager: 2.09 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: 1685 1.34 - 1.46: 1215 1.46 - 1.58: 2547 1.58 - 1.70: 22 1.70 - 1.82: 28 Bond restraints: 5497 Sorted by residual: bond pdb=" OG1 TPO V 360 " pdb=" P TPO V 360 " ideal model delta sigma weight residual 1.717 1.605 0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" OG1 TPO V 359 " pdb=" P TPO V 359 " ideal model delta sigma weight residual 1.717 1.625 0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" O1P TPO V 359 " pdb=" P TPO V 359 " ideal model delta sigma weight residual 1.525 1.610 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" O2P TPO V 359 " pdb=" P TPO V 359 " ideal model delta sigma weight residual 1.528 1.607 -0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" O2P TPO V 360 " pdb=" P TPO V 360 " ideal model delta sigma weight residual 1.528 1.605 -0.077 2.00e-02 2.50e+03 1.47e+01 ... (remaining 5492 not shown) Histogram of bond angle deviations from ideal: 97.88 - 105.15: 124 105.15 - 112.42: 2796 112.42 - 119.69: 1867 119.69 - 126.95: 2634 126.95 - 134.22: 67 Bond angle restraints: 7488 Sorted by residual: angle pdb=" N GLU B 156 " pdb=" CA GLU B 156 " pdb=" C GLU B 156 " ideal model delta sigma weight residual 110.24 117.78 -7.54 1.41e+00 5.03e-01 2.86e+01 angle pdb=" C THR B 74 " pdb=" N PHE B 75 " pdb=" CA PHE B 75 " ideal model delta sigma weight residual 122.29 130.49 -8.20 1.65e+00 3.67e-01 2.47e+01 angle pdb=" C GLN B 189 " pdb=" N PHE B 190 " pdb=" CA PHE B 190 " ideal model delta sigma weight residual 122.07 112.79 9.28 2.01e+00 2.48e-01 2.13e+01 angle pdb=" CA LEU A 85 " pdb=" CB LEU A 85 " pdb=" CG LEU A 85 " ideal model delta sigma weight residual 116.30 100.64 15.66 3.50e+00 8.16e-02 2.00e+01 angle pdb=" N PHE B 75 " pdb=" CA PHE B 75 " pdb=" C PHE B 75 " ideal model delta sigma weight residual 109.23 102.62 6.61 1.55e+00 4.16e-01 1.82e+01 ... (remaining 7483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.64: 3059 13.64 - 27.29: 185 27.29 - 40.93: 30 40.93 - 54.58: 7 54.58 - 68.22: 4 Dihedral angle restraints: 3285 sinusoidal: 1239 harmonic: 2046 Sorted by residual: dihedral pdb=" CA ALA A 51 " pdb=" C ALA A 51 " pdb=" N THR A 52 " pdb=" CA THR A 52 " ideal model delta harmonic sigma weight residual 180.00 144.84 35.16 0 5.00e+00 4.00e-02 4.95e+01 dihedral pdb=" CA TYR A 59 " pdb=" C TYR A 59 " pdb=" N ALA A 60 " pdb=" CA ALA A 60 " ideal model delta harmonic sigma weight residual 180.00 154.38 25.62 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA SER A 50 " pdb=" C SER A 50 " pdb=" N ALA A 51 " pdb=" CA ALA A 51 " ideal model delta harmonic sigma weight residual 180.00 154.98 25.02 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 3282 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 641 0.077 - 0.154: 188 0.154 - 0.231: 23 0.231 - 0.308: 2 0.308 - 0.385: 2 Chirality restraints: 856 Sorted by residual: chirality pdb=" CB VAL B 164 " pdb=" CA VAL B 164 " pdb=" CG1 VAL B 164 " pdb=" CG2 VAL B 164 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CA GLU B 156 " pdb=" N GLU B 156 " pdb=" C GLU B 156 " pdb=" CB GLU B 156 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA VAL B 164 " pdb=" N VAL B 164 " pdb=" C VAL B 164 " pdb=" CB VAL B 164 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 853 not shown) Planarity restraints: 951 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 9 " 0.028 2.00e-02 2.50e+03 2.35e-02 9.65e+00 pdb=" CG PHE B 9 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE B 9 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE B 9 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE B 9 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 9 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 9 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 113 " 0.022 2.00e-02 2.50e+03 2.04e-02 8.32e+00 pdb=" CG TYR B 113 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR B 113 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 113 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 113 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 113 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR B 113 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 113 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 21 " 0.019 2.00e-02 2.50e+03 1.97e-02 7.76e+00 pdb=" CG TYR B 21 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR B 21 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR B 21 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 21 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 21 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR B 21 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR B 21 " -0.005 2.00e-02 2.50e+03 ... (remaining 948 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1070 2.78 - 3.31: 4517 3.31 - 3.84: 8675 3.84 - 4.37: 9386 4.37 - 4.90: 16519 Nonbonded interactions: 40167 Sorted by model distance: nonbonded pdb=" OD1 ASP B 204 " pdb=" OH TYR B 208 " model vdw 2.245 2.440 nonbonded pdb=" O ASP A 89 " pdb=" OH TYR A 93 " model vdw 2.256 2.440 nonbonded pdb=" OG SEP V 363 " pdb=" N SEP V 364 " model vdw 2.314 2.520 nonbonded pdb=" O ASP L 83 " pdb=" OH TYR L 87 " model vdw 2.318 2.440 nonbonded pdb=" OD1 ASP H 76 " pdb=" OG SER H 78 " model vdw 2.337 2.440 ... (remaining 40162 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 3.130 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 18.610 Find NCS groups from input model: 0.160 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 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 : 0.010 0.121 5497 Z= 0.621 Angle : 1.327 15.660 7488 Z= 0.729 Chirality : 0.070 0.385 856 Planarity : 0.007 0.055 951 Dihedral : 9.614 68.220 1967 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.74 % Favored : 93.11 % Rotamer: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.50 (0.31), residues: 682 helix: -0.31 (1.30), residues: 12 sheet: -0.88 (0.30), residues: 271 loop : -1.06 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP A 36 HIS 0.012 0.004 HIS A 44 PHE 0.054 0.005 PHE B 9 TYR 0.051 0.005 TYR B 113 ARG 0.015 0.002 ARG H 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.6443 (tpt-90) cc_final: 0.6016 (tpp80) REVERT: A 64 LYS cc_start: 0.8636 (ptpt) cc_final: 0.8060 (ptpp) REVERT: A 67 PHE cc_start: 0.7543 (m-10) cc_final: 0.7182 (m-10) REVERT: A 85 LEU cc_start: 0.7294 (mt) cc_final: 0.7091 (mt) REVERT: B 42 LEU cc_start: 0.7307 (tp) cc_final: 0.6995 (pp) REVERT: B 77 LYS cc_start: 0.8015 (tppt) cc_final: 0.7525 (mmtm) REVERT: B 232 LYS cc_start: 0.6625 (mttt) cc_final: 0.5500 (tttt) REVERT: H 48 LEU cc_start: 0.9402 (mt) cc_final: 0.9089 (tp) REVERT: H 71 PHE cc_start: 0.8088 (m-10) cc_final: 0.6749 (m-10) REVERT: L 25 ARG cc_start: 0.8411 (ttm170) cc_final: 0.8169 (mtm-85) REVERT: L 28 GLN cc_start: 0.8997 (tt0) cc_final: 0.8639 (mt0) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1979 time to fit residues: 37.2886 Evaluate side-chains 75 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 81 GLN B 85 GLN ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5497 Z= 0.253 Angle : 0.727 12.289 7488 Z= 0.372 Chirality : 0.046 0.154 856 Planarity : 0.005 0.058 951 Dihedral : 6.838 56.395 780 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.63 % Allowed : 12.63 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % 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 (0.32), residues: 682 helix: 0.32 (1.45), residues: 12 sheet: -0.14 (0.31), residues: 281 loop : -0.47 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 36 HIS 0.009 0.002 HIS B 219 PHE 0.013 0.002 PHE B 9 TYR 0.032 0.002 TYR H 57 ARG 0.008 0.001 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: A 19 ARG cc_start: 0.6583 (tpt-90) cc_final: 0.6173 (tpp80) REVERT: A 22 CYS cc_start: 0.6799 (t) cc_final: 0.6242 (m) REVERT: A 64 LYS cc_start: 0.8518 (ptpt) cc_final: 0.8256 (ptpp) REVERT: A 75 LYS cc_start: 0.8430 (tttt) cc_final: 0.8157 (ttmt) REVERT: A 82 MET cc_start: 0.8158 (mtp) cc_final: 0.7490 (mtp) REVERT: B 77 LYS cc_start: 0.8188 (tppt) cc_final: 0.7763 (mmtm) REVERT: B 185 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7070 (mt-10) REVERT: B 232 LYS cc_start: 0.6131 (mttt) cc_final: 0.5547 (mttt) REVERT: L 28 GLN cc_start: 0.8945 (tt0) cc_final: 0.8582 (mt0) REVERT: L 82 GLU cc_start: 0.8462 (pm20) cc_final: 0.8118 (pp20) outliers start: 15 outliers final: 11 residues processed: 106 average time/residue: 0.1838 time to fit residues: 24.7544 Evaluate side-chains 81 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 70 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 21 optimal weight: 0.0020 chunk 49 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5497 Z= 0.252 Angle : 0.659 8.508 7488 Z= 0.338 Chirality : 0.045 0.159 856 Planarity : 0.004 0.050 951 Dihedral : 6.568 56.236 780 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.56 % Allowed : 12.46 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % 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: -0.25 (0.32), residues: 682 helix: 1.28 (1.53), residues: 12 sheet: 0.19 (0.31), residues: 274 loop : -0.41 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 36 HIS 0.009 0.002 HIS B 219 PHE 0.014 0.002 PHE A 67 TYR 0.025 0.002 TYR H 83 ARG 0.005 0.001 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 85 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 CYS cc_start: 0.6874 (t) cc_final: 0.6466 (m) REVERT: A 67 PHE cc_start: 0.7485 (m-10) cc_final: 0.7158 (m-10) REVERT: A 82 MET cc_start: 0.7990 (mtp) cc_final: 0.7503 (mtp) REVERT: B 202 SER cc_start: 0.7751 (p) cc_final: 0.6767 (t) REVERT: B 225 ASN cc_start: 0.8505 (m110) cc_final: 0.8155 (p0) REVERT: H 48 LEU cc_start: 0.9417 (mp) cc_final: 0.9152 (mt) REVERT: L 28 GLN cc_start: 0.8994 (tt0) cc_final: 0.8655 (mt0) REVERT: L 82 GLU cc_start: 0.8425 (pm20) cc_final: 0.8094 (pp20) outliers start: 26 outliers final: 17 residues processed: 99 average time/residue: 0.1707 time to fit residues: 22.1436 Evaluate side-chains 88 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 71 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 0.0060 chunk 29 optimal weight: 0.0040 chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 65 optimal weight: 0.0000 chunk 58 optimal weight: 1.9990 chunk 17 optimal weight: 0.0070 chunk 54 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.1830 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN B 159 HIS ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5497 Z= 0.137 Angle : 0.594 7.521 7488 Z= 0.296 Chirality : 0.044 0.140 856 Planarity : 0.004 0.045 951 Dihedral : 6.130 52.411 780 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.16 % Allowed : 15.26 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % 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: 0.02 (0.32), residues: 682 helix: 2.04 (1.68), residues: 12 sheet: 0.60 (0.32), residues: 259 loop : -0.42 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 36 HIS 0.008 0.001 HIS B 219 PHE 0.013 0.002 PHE B 268 TYR 0.017 0.001 TYR H 83 ARG 0.004 0.000 ARG B 282 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 84 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.8008 (mtp) cc_final: 0.7659 (mtp) REVERT: B 225 ASN cc_start: 0.8374 (m110) cc_final: 0.8007 (p0) REVERT: H 48 LEU cc_start: 0.9346 (mp) cc_final: 0.9103 (tp) REVERT: L 28 GLN cc_start: 0.8986 (tt0) cc_final: 0.8697 (mt0) outliers start: 18 outliers final: 10 residues processed: 96 average time/residue: 0.1407 time to fit residues: 18.4222 Evaluate side-chains 75 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 33 optimal weight: 0.5980 chunk 58 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 22 optimal weight: 0.0270 chunk 59 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 overall best weight: 2.0842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5497 Z= 0.288 Angle : 0.674 8.765 7488 Z= 0.340 Chirality : 0.046 0.229 856 Planarity : 0.004 0.039 951 Dihedral : 6.409 58.500 780 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.74 % Allowed : 16.84 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % 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: -0.01 (0.33), residues: 682 helix: 1.96 (1.63), residues: 12 sheet: 0.50 (0.32), residues: 276 loop : -0.41 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 36 HIS 0.007 0.001 HIS A 44 PHE 0.021 0.002 PHE A 67 TYR 0.018 0.002 TYR H 83 ARG 0.004 0.001 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 69 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 225 ASN cc_start: 0.8359 (m110) cc_final: 0.8127 (p0) REVERT: B 324 LYS cc_start: 0.7641 (tttt) cc_final: 0.7295 (tttp) REVERT: H 23 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7364 (mm) REVERT: H 48 LEU cc_start: 0.9443 (mp) cc_final: 0.9212 (mt) REVERT: L 28 GLN cc_start: 0.9068 (tt0) cc_final: 0.8760 (mt0) REVERT: L 82 GLU cc_start: 0.8439 (pm20) cc_final: 0.7806 (pp20) outliers start: 27 outliers final: 22 residues processed: 92 average time/residue: 0.1587 time to fit residues: 19.4934 Evaluate side-chains 87 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 64 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 0.0770 chunk 16 optimal weight: 4.9990 chunk 65 optimal weight: 0.4980 chunk 54 optimal weight: 0.1980 chunk 30 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 overall best weight: 1.1540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5497 Z= 0.197 Angle : 0.632 9.484 7488 Z= 0.309 Chirality : 0.045 0.217 856 Planarity : 0.004 0.037 951 Dihedral : 6.267 55.243 780 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.16 % Allowed : 18.60 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % 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: 0.05 (0.33), residues: 682 helix: 2.30 (1.63), residues: 12 sheet: 0.73 (0.33), residues: 257 loop : -0.47 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 36 HIS 0.003 0.001 HIS A 44 PHE 0.011 0.001 PHE B 268 TYR 0.016 0.002 TYR H 83 ARG 0.003 0.000 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 75 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7822 (tmm) cc_final: 0.7471 (tmm) REVERT: A 109 GLN cc_start: 0.8770 (mp10) cc_final: 0.8546 (mp10) REVERT: B 215 SER cc_start: 0.8932 (m) cc_final: 0.8391 (p) REVERT: B 225 ASN cc_start: 0.8241 (m110) cc_final: 0.7981 (p0) REVERT: B 326 LYS cc_start: 0.7465 (tttt) cc_final: 0.6831 (tttt) REVERT: H 48 LEU cc_start: 0.9425 (mp) cc_final: 0.9113 (tp) REVERT: L 28 GLN cc_start: 0.9040 (tt0) cc_final: 0.8775 (mt0) REVERT: L 82 GLU cc_start: 0.8426 (pm20) cc_final: 0.7796 (pp20) outliers start: 18 outliers final: 17 residues processed: 86 average time/residue: 0.1516 time to fit residues: 17.5992 Evaluate side-chains 87 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 70 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 0.1980 chunk 37 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 65 optimal weight: 0.4980 chunk 41 optimal weight: 5.9990 chunk 39 optimal weight: 0.0270 chunk 30 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 26 optimal weight: 0.1980 chunk 19 optimal weight: 0.8980 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5497 Z= 0.142 Angle : 0.597 8.805 7488 Z= 0.287 Chirality : 0.044 0.203 856 Planarity : 0.004 0.040 951 Dihedral : 5.955 59.324 780 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.63 % Allowed : 18.95 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % 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: 0.10 (0.33), residues: 682 helix: 0.53 (1.39), residues: 18 sheet: 0.79 (0.32), residues: 268 loop : -0.45 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 36 HIS 0.001 0.000 HIS B 30 PHE 0.011 0.001 PHE B 268 TYR 0.013 0.001 TYR B 249 ARG 0.002 0.000 ARG L 25 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 78 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8434 (tttt) cc_final: 0.8048 (tptt) REVERT: A 109 GLN cc_start: 0.8804 (mp10) cc_final: 0.8538 (mp10) REVERT: B 185 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7591 (tm-30) REVERT: B 215 SER cc_start: 0.8995 (m) cc_final: 0.8451 (p) REVERT: B 225 ASN cc_start: 0.8415 (m110) cc_final: 0.8071 (p0) REVERT: B 255 MET cc_start: 0.5934 (ttm) cc_final: 0.5682 (tpp) REVERT: B 326 LYS cc_start: 0.7368 (tttt) cc_final: 0.6774 (tttt) REVERT: H 48 LEU cc_start: 0.9386 (mp) cc_final: 0.9128 (tp) REVERT: L 82 GLU cc_start: 0.8356 (pm20) cc_final: 0.7819 (pp20) outliers start: 15 outliers final: 13 residues processed: 86 average time/residue: 0.1743 time to fit residues: 19.6794 Evaluate side-chains 84 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 71 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain L residue 6 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 57 optimal weight: 0.0030 chunk 61 optimal weight: 0.1980 chunk 36 optimal weight: 10.0000 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.5073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5497 Z= 0.162 Angle : 0.596 7.978 7488 Z= 0.288 Chirality : 0.044 0.196 856 Planarity : 0.004 0.039 951 Dihedral : 5.891 57.219 780 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.46 % Allowed : 19.65 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % 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: 0.33 (0.33), residues: 682 helix: 0.76 (1.39), residues: 18 sheet: 0.94 (0.32), residues: 279 loop : -0.33 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 36 HIS 0.002 0.000 HIS A 44 PHE 0.010 0.001 PHE B 268 TYR 0.012 0.001 TYR H 83 ARG 0.002 0.000 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.6354 (m-80) cc_final: 0.5782 (m-80) REVERT: A 75 LYS cc_start: 0.8412 (tttt) cc_final: 0.8007 (tptt) REVERT: A 109 GLN cc_start: 0.8798 (mp10) cc_final: 0.8510 (mp10) REVERT: B 185 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7550 (tm-30) REVERT: B 215 SER cc_start: 0.9011 (m) cc_final: 0.8448 (p) REVERT: B 225 ASN cc_start: 0.8312 (m110) cc_final: 0.7963 (p0) REVERT: B 243 LEU cc_start: 0.6909 (OUTLIER) cc_final: 0.5429 (pt) REVERT: B 326 LYS cc_start: 0.7337 (tttt) cc_final: 0.6675 (tttt) REVERT: H 48 LEU cc_start: 0.9404 (mp) cc_final: 0.9161 (tp) REVERT: L 82 GLU cc_start: 0.8283 (pm20) cc_final: 0.7815 (pp20) outliers start: 14 outliers final: 11 residues processed: 83 average time/residue: 0.1741 time to fit residues: 19.0381 Evaluate side-chains 82 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 76 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 0.9980 chunk 47 optimal weight: 0.0980 chunk 18 optimal weight: 0.0030 chunk 55 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 64 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.5229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5497 Z= 0.151 Angle : 0.603 9.329 7488 Z= 0.288 Chirality : 0.043 0.183 856 Planarity : 0.004 0.039 951 Dihedral : 5.670 51.650 780 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.46 % Allowed : 19.65 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % 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: 0.39 (0.33), residues: 682 helix: 0.72 (1.39), residues: 18 sheet: 1.04 (0.32), residues: 276 loop : -0.33 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 36 HIS 0.004 0.001 HIS A 44 PHE 0.050 0.002 PHE A 27 TYR 0.010 0.001 TYR H 83 ARG 0.002 0.000 ARG H 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 70 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.7965 (pm20) cc_final: 0.7734 (pm20) REVERT: A 75 LYS cc_start: 0.8407 (tttt) cc_final: 0.8078 (tptt) REVERT: A 109 GLN cc_start: 0.8803 (mp10) cc_final: 0.8510 (mp10) REVERT: B 185 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7528 (tm-30) REVERT: B 215 SER cc_start: 0.8926 (m) cc_final: 0.8444 (p) REVERT: B 225 ASN cc_start: 0.8282 (m110) cc_final: 0.7926 (p0) REVERT: B 255 MET cc_start: 0.6263 (ttm) cc_final: 0.5973 (tpp) REVERT: B 326 LYS cc_start: 0.7312 (tttt) cc_final: 0.6658 (tttt) REVERT: H 48 LEU cc_start: 0.9387 (mp) cc_final: 0.9166 (tp) REVERT: H 84 LEU cc_start: 0.8300 (mp) cc_final: 0.8026 (mp) REVERT: L 82 GLU cc_start: 0.8249 (pm20) cc_final: 0.7803 (pp20) outliers start: 14 outliers final: 14 residues processed: 78 average time/residue: 0.1632 time to fit residues: 17.0308 Evaluate side-chains 83 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 69 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain L residue 21 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 67 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 57 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.5265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5497 Z= 0.210 Angle : 0.624 10.766 7488 Z= 0.305 Chirality : 0.044 0.178 856 Planarity : 0.004 0.038 951 Dihedral : 5.860 54.023 780 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.81 % Allowed : 19.82 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % 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: 0.34 (0.33), residues: 682 helix: 0.80 (1.41), residues: 18 sheet: 0.94 (0.31), residues: 277 loop : -0.32 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 36 HIS 0.005 0.001 HIS A 44 PHE 0.020 0.002 PHE A 27 TYR 0.013 0.001 TYR H 83 ARG 0.006 0.000 ARG H 41 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 68 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.6423 (m-80) cc_final: 0.5993 (m-10) REVERT: A 75 LYS cc_start: 0.8371 (tttt) cc_final: 0.8053 (tptt) REVERT: A 109 GLN cc_start: 0.8796 (mp10) cc_final: 0.8519 (mp10) REVERT: B 185 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7548 (tm-30) REVERT: B 215 SER cc_start: 0.8994 (m) cc_final: 0.8471 (p) REVERT: B 225 ASN cc_start: 0.8227 (m110) cc_final: 0.7932 (p0) REVERT: B 243 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.5349 (pt) REVERT: B 326 LYS cc_start: 0.7413 (tttt) cc_final: 0.6715 (tttt) REVERT: H 48 LEU cc_start: 0.9428 (mp) cc_final: 0.9175 (mt) REVERT: H 84 LEU cc_start: 0.8259 (mp) cc_final: 0.7967 (mp) REVERT: L 82 GLU cc_start: 0.8302 (pm20) cc_final: 0.7869 (pp20) outliers start: 16 outliers final: 15 residues processed: 78 average time/residue: 0.1614 time to fit residues: 16.8725 Evaluate side-chains 82 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 66 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain L residue 21 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 14 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 55 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 61 optimal weight: 0.0980 chunk 36 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.112203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.097166 restraints weight = 19121.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.099476 restraints weight = 11806.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.101110 restraints weight = 8297.495| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.5408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5497 Z= 0.160 Angle : 0.612 10.991 7488 Z= 0.294 Chirality : 0.044 0.178 856 Planarity : 0.004 0.039 951 Dihedral : 5.742 53.128 780 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.63 % Allowed : 20.18 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % 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: 0.40 (0.33), residues: 682 helix: 0.94 (1.42), residues: 18 sheet: 1.01 (0.31), residues: 277 loop : -0.31 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 36 HIS 0.007 0.001 HIS A 44 PHE 0.052 0.002 PHE A 27 TYR 0.012 0.001 TYR H 83 ARG 0.005 0.000 ARG H 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1425.43 seconds wall clock time: 26 minutes 17.05 seconds (1577.05 seconds total)