Starting phenix.real_space_refine on Fri Apr 5 20:48:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ure_26710/04_2024/7ure_26710_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ure_26710/04_2024/7ure_26710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ure_26710/04_2024/7ure_26710.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ure_26710/04_2024/7ure_26710.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ure_26710/04_2024/7ure_26710_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ure_26710/04_2024/7ure_26710_updated.pdb" } resolution = 3.19 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= 0.005 sd= 0.092 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 35 5.16 5 C 3566 2.51 5 N 895 2.21 5 O 953 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 124": "NH1" <-> "NH2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 271": "OE1" <-> "OE2" Residue "A ARG 318": "NH1" <-> "NH2" Residue "A PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 413": "OD1" <-> "OD2" Residue "L PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 47": "OE1" <-> "OE2" Residue "L TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 108": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 5450 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3465 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 14, 'TRANS': 417} Chain breaks: 2 Chain: "L" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "H" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 926 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "B" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 158 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DNP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {' ZN': 1, 'AJP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'PAM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PAM:plan-1': 1} Unresolved non-hydrogen planarities: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2849 SG CYS A 370 54.825 29.237 18.480 1.00101.61 S ATOM 2896 SG CYS A 376 53.706 28.652 22.060 1.00110.68 S Time building chain proxies: 3.72, per 1000 atoms: 0.68 Number of scatterers: 5450 At special positions: 0 Unit cell: (97.11, 70.55, 97.11, 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) Zn 1 29.99 S 35 16.00 O 953 8.00 N 895 7.00 C 3566 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 17 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 108 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 217 " distance=2.03 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS B 212 " distance=2.03 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: 2.10 Conformation dependent library (CDL) restraints added in 951.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" ND1 HIS A 382 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 370 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 376 " 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1254 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 19 helices and 8 sheets defined 46.0% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 6 through 44 removed outlier: 4.015A pdb=" N GLN A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU A 14 " --> pdb=" O PHE A 10 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N GLN A 15 " --> pdb=" O GLN A 11 " (cutoff:3.500A) Proline residue: A 20 - end of helix removed outlier: 5.369A pdb=" N LEU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LEU A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG A 44 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 67 Processing helix chain 'A' and resid 71 through 88 removed outlier: 3.569A pdb=" N LEU A 88 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 111 Processing helix chain 'A' and resid 117 through 143 removed outlier: 5.316A pdb=" N GLY A 125 " --> pdb=" O HIS A 121 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ALA A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 187 through 209 Processing helix chain 'A' and resid 237 through 264 Processing helix chain 'A' and resid 284 through 287 No H-bonds generated for 'chain 'A' and resid 284 through 287' Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 302 through 319 removed outlier: 5.327A pdb=" N ARG A 318 " --> pdb=" O LYS A 314 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU A 319 " --> pdb=" O ASN A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 335 Processing helix chain 'A' and resid 344 through 366 Processing helix chain 'A' and resid 389 through 412 removed outlier: 4.531A pdb=" N LEU A 411 " --> pdb=" O TYR A 407 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N PHE A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 436 Processing helix chain 'A' and resid 440 through 455 Processing helix chain 'L' and resid 100 through 102 No H-bonds generated for 'chain 'L' and resid 100 through 102' Processing helix chain 'H' and resid 48 through 50 No H-bonds generated for 'chain 'H' and resid 48 through 50' Processing sheet with id= A, first strand: chain 'A' and resid 269 through 271 removed outlier: 3.679A pdb=" N GLU A 276 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'L' and resid 24 through 27 removed outlier: 4.126A pdb=" N GLN L 90 " --> pdb=" O SER L 87 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER L 87 " --> pdb=" O GLN L 90 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER L 92 " --> pdb=" O SER L 85 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'L' and resid 30 through 33 removed outlier: 6.165A pdb=" N LYS L 123 " --> pdb=" O LEU L 31 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ALA L 33 " --> pdb=" O LYS L 123 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLU L 125 " --> pdb=" O ALA L 33 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'L' and resid 53 through 58 Processing sheet with id= E, first strand: chain 'H' and resid 29 through 31 removed outlier: 3.728A pdb=" N TYR H 113 " --> pdb=" O THR H 132 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LYS H 57 " --> pdb=" O TRP H 66 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N TRP H 66 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER H 76 " --> pdb=" O ASN H 71 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 36 through 42 Processing sheet with id= G, first strand: chain 'H' and resid 116 through 118 removed outlier: 3.905A pdb=" N TYR H 127 " --> pdb=" O ARG H 117 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 202 through 206 removed outlier: 3.502A pdb=" N TRP B 218 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS B 204 " --> pdb=" O THR B 216 " (cutoff:3.500A) 281 hydrogen bonds defined for protein. 768 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: 2.07 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.20: 5 1.20 - 1.40: 2365 1.40 - 1.60: 3182 1.60 - 1.79: 21 1.79 - 1.99: 39 Bond restraints: 5612 Sorted by residual: bond pdb=" C07 AJP A 501 " pdb=" C08 AJP A 501 " ideal model delta sigma weight residual 1.550 1.991 -0.441 2.00e-02 2.50e+03 4.86e+02 bond pdb=" C01 AJP A 501 " pdb=" C02 AJP A 501 " ideal model delta sigma weight residual 1.521 1.950 -0.429 2.00e-02 2.50e+03 4.59e+02 bond pdb=" C08 AJP A 501 " pdb=" O09 AJP A 501 " ideal model delta sigma weight residual 1.410 1.002 0.408 2.00e-02 2.50e+03 4.16e+02 bond pdb=" C05 AJP A 501 " pdb=" O09 AJP A 501 " ideal model delta sigma weight residual 1.407 1.803 -0.396 2.00e-02 2.50e+03 3.92e+02 bond pdb=" C02 AJP A 501 " pdb=" C03 AJP A 501 " ideal model delta sigma weight residual 1.525 1.130 0.395 2.00e-02 2.50e+03 3.91e+02 ... (remaining 5607 not shown) Histogram of bond angle deviations from ideal: 98.92 - 105.95: 107 105.95 - 112.97: 3066 112.97 - 120.00: 1887 120.00 - 127.03: 2483 127.03 - 134.05: 87 Bond angle restraints: 7630 Sorted by residual: angle pdb=" C2 PAM B 601 " pdb=" C1 PAM B 601 " pdb=" O1 PAM B 601 " ideal model delta sigma weight residual 115.96 98.92 17.04 3.00e+00 1.11e-01 3.23e+01 angle pdb=" C11 AJP A 501 " pdb=" C12 AJP A 501 " pdb=" C81 AJP A 501 " ideal model delta sigma weight residual 114.35 100.70 13.65 3.00e+00 1.11e-01 2.07e+01 angle pdb=" C03 AJP A 501 " pdb=" C02 AJP A 501 " pdb=" C85 AJP A 501 " ideal model delta sigma weight residual 109.14 122.46 -13.32 3.00e+00 1.11e-01 1.97e+01 angle pdb=" C04 AJP A 501 " pdb=" C05 AJP A 501 " pdb=" O84 AJP A 501 " ideal model delta sigma weight residual 111.01 122.20 -11.19 3.00e+00 1.11e-01 1.39e+01 angle pdb=" C06 AJP A 501 " pdb=" C07 AJP A 501 " pdb=" C12 AJP A 501 " ideal model delta sigma weight residual 120.30 130.92 -10.62 3.00e+00 1.11e-01 1.25e+01 ... (remaining 7625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.23: 3179 35.23 - 70.45: 83 70.45 - 105.68: 24 105.68 - 140.90: 35 140.90 - 176.13: 9 Dihedral angle restraints: 3330 sinusoidal: 1368 harmonic: 1962 Sorted by residual: dihedral pdb=" C06 AJP A 501 " pdb=" C07 AJP A 501 " pdb=" C12 AJP A 501 " pdb=" C13 AJP A 501 " ideal model delta sinusoidal sigma weight residual 109.15 -74.72 -176.13 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C29 AJP A 501 " pdb=" C30 AJP A 501 " pdb=" C32 AJP A 501 " pdb=" O33 AJP A 501 " ideal model delta sinusoidal sigma weight residual -60.96 108.71 -169.67 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C08 AJP A 501 " pdb=" C07 AJP A 501 " pdb=" C12 AJP A 501 " pdb=" C81 AJP A 501 " ideal model delta sinusoidal sigma weight residual 101.32 -65.22 166.54 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 3327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.102: 832 1.102 - 2.205: 0 2.205 - 3.307: 0 3.307 - 4.409: 2 4.409 - 5.512: 19 Chirality restraints: 853 Sorted by residual: chirality pdb=" C15 AJP A 501 " pdb=" C14 AJP A 501 " pdb=" C16 AJP A 501 " pdb=" C20 AJP A 501 " both_signs ideal model delta sigma weight residual False -2.42 3.09 -5.51 2.00e-01 2.50e+01 7.59e+02 chirality pdb=" C20 AJP A 501 " pdb=" C15 AJP A 501 " pdb=" C19 AJP A 501 " pdb=" C21 AJP A 501 " both_signs ideal model delta sigma weight residual False 2.96 -2.52 5.48 2.00e-01 2.50e+01 7.51e+02 chirality pdb=" C16 AJP A 501 " pdb=" C11 AJP A 501 " pdb=" C15 AJP A 501 " pdb=" C17 AJP A 501 " both_signs ideal model delta sigma weight residual False -2.70 2.76 -5.47 2.00e-01 2.50e+01 7.47e+02 ... (remaining 850 not shown) Planarity restraints: 921 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 310 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.00e+00 pdb=" C ASN A 310 " 0.039 2.00e-02 2.50e+03 pdb=" O ASN A 310 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR A 311 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 309 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.44e+00 pdb=" C ASN A 309 " 0.036 2.00e-02 2.50e+03 pdb=" O ASN A 309 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN A 310 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 215 " -0.033 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO A 216 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 216 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 216 " -0.028 5.00e-02 4.00e+02 ... (remaining 918 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 85 2.67 - 3.23: 5209 3.23 - 3.79: 8459 3.79 - 4.34: 11555 4.34 - 4.90: 19542 Nonbonded interactions: 44850 Sorted by model distance: nonbonded pdb=" O LEU A 319 " pdb=" OG SER A 323 " model vdw 2.118 2.440 nonbonded pdb=" O33 AJP A 501 " pdb=" O40 AJP A 501 " model vdw 2.265 2.440 nonbonded pdb=" O ARG A 90 " pdb=" NH1 ARG A 95 " model vdw 2.276 2.520 nonbonded pdb=" O PHE A 340 " pdb=" ND1 HIS A 341 " model vdw 2.276 2.520 nonbonded pdb=" ND1 HIS A 53 " pdb=" OH TYR A 176 " model vdw 2.315 2.520 ... (remaining 44845 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.790 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 20.750 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.060 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 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 : 0.017 0.441 5612 Z= 1.343 Angle : 0.781 17.041 7630 Z= 0.350 Chirality : 0.778 5.512 853 Planarity : 0.005 0.049 921 Dihedral : 25.750 176.131 2061 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.30), residues: 663 helix: -0.41 (0.25), residues: 331 sheet: -2.23 (0.46), residues: 125 loop : -2.62 (0.40), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 66 HIS 0.005 0.001 HIS L 111 PHE 0.010 0.001 PHE A 268 TYR 0.016 0.002 TYR A 83 ARG 0.002 0.000 ARG H 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.594 Fit side-chains revert: symmetry clash REVERT: A 62 PHE cc_start: 0.8162 (t80) cc_final: 0.7925 (t80) REVERT: A 201 LEU cc_start: 0.7965 (mt) cc_final: 0.7760 (mm) REVERT: A 407 TYR cc_start: 0.8170 (t80) cc_final: 0.7481 (t80) REVERT: A 434 TRP cc_start: 0.8298 (m-10) cc_final: 0.8018 (m-10) REVERT: A 452 TYR cc_start: 0.6613 (t80) cc_final: 0.6403 (t80) REVERT: L 116 TYR cc_start: 0.9007 (m-80) cc_final: 0.8725 (m-80) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.2206 time to fit residues: 22.9249 Evaluate side-chains 73 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 71 HIS A 91 HIS A 121 HIS A 127 GLN A 181 GLN A 315 ASN A 394 ASN L 96 ASN L 111 HIS H 22 GLN ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 ASN H 78 ASN ** H 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5612 Z= 0.246 Angle : 1.123 34.403 7630 Z= 0.433 Chirality : 0.122 2.297 853 Planarity : 0.005 0.045 921 Dihedral : 21.191 174.951 893 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.69 % Allowed : 10.52 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.92 (0.32), residues: 663 helix: 0.78 (0.27), residues: 327 sheet: -1.76 (0.44), residues: 135 loop : -1.98 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 66 HIS 0.006 0.001 HIS L 111 PHE 0.010 0.001 PHE A 268 TYR 0.016 0.002 TYR A 311 ARG 0.002 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 0.601 Fit side-chains REVERT: A 62 PHE cc_start: 0.8164 (t80) cc_final: 0.7926 (t80) REVERT: A 112 MET cc_start: 0.5992 (tmm) cc_final: 0.5791 (ttm) REVERT: A 341 HIS cc_start: 0.7998 (OUTLIER) cc_final: 0.7232 (p-80) REVERT: A 407 TYR cc_start: 0.8191 (t80) cc_final: 0.7451 (t80) REVERT: A 434 TRP cc_start: 0.8325 (m-10) cc_final: 0.8024 (m-10) REVERT: A 452 TYR cc_start: 0.6679 (t80) cc_final: 0.6448 (t80) REVERT: L 116 TYR cc_start: 0.8998 (m-80) cc_final: 0.8745 (m-80) REVERT: B 217 CYS cc_start: 0.6914 (m) cc_final: 0.6662 (m) outliers start: 4 outliers final: 2 residues processed: 76 average time/residue: 0.2058 time to fit residues: 20.0564 Evaluate side-chains 70 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 341 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 53 optimal weight: 0.1980 chunk 59 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 48 optimal weight: 0.0670 overall best weight: 1.0524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5612 Z= 0.217 Angle : 1.101 34.900 7630 Z= 0.420 Chirality : 0.120 2.224 853 Planarity : 0.005 0.045 921 Dihedral : 20.648 175.789 893 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.07 % Allowed : 11.90 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.33 (0.33), residues: 663 helix: 1.28 (0.28), residues: 325 sheet: -1.49 (0.44), residues: 135 loop : -1.69 (0.44), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 66 HIS 0.003 0.001 HIS A 94 PHE 0.009 0.001 PHE A 248 TYR 0.021 0.002 TYR L 52 ARG 0.003 0.000 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 0.573 Fit side-chains REVERT: A 62 PHE cc_start: 0.8132 (t80) cc_final: 0.7906 (t80) REVERT: A 123 MET cc_start: 0.7866 (mtm) cc_final: 0.7665 (mtm) REVERT: A 341 HIS cc_start: 0.7950 (OUTLIER) cc_final: 0.7145 (p-80) REVERT: A 452 TYR cc_start: 0.6698 (t80) cc_final: 0.6466 (t80) REVERT: B 217 CYS cc_start: 0.7016 (m) cc_final: 0.6784 (m) outliers start: 12 outliers final: 7 residues processed: 80 average time/residue: 0.2067 time to fit residues: 21.1480 Evaluate side-chains 80 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain B residue 214 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 123 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5612 Z= 0.188 Angle : 1.099 34.644 7630 Z= 0.416 Chirality : 0.118 2.173 853 Planarity : 0.004 0.043 921 Dihedral : 20.511 176.135 893 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.90 % Allowed : 13.62 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.01 (0.34), residues: 663 helix: 1.52 (0.28), residues: 323 sheet: -1.27 (0.44), residues: 134 loop : -1.53 (0.45), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 66 HIS 0.003 0.001 HIS L 111 PHE 0.009 0.001 PHE A 248 TYR 0.015 0.001 TYR H 74 ARG 0.002 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 69 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: A 62 PHE cc_start: 0.8104 (t80) cc_final: 0.7891 (t80) REVERT: A 341 HIS cc_start: 0.7910 (OUTLIER) cc_final: 0.7096 (p-80) REVERT: A 452 TYR cc_start: 0.6677 (t80) cc_final: 0.6432 (t80) REVERT: B 217 CYS cc_start: 0.6987 (m) cc_final: 0.6761 (m) outliers start: 11 outliers final: 8 residues processed: 76 average time/residue: 0.2157 time to fit residues: 20.8795 Evaluate side-chains 75 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain B residue 214 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 0.0270 chunk 0 optimal weight: 6.9990 chunk 47 optimal weight: 0.0060 chunk 26 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.2060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5612 Z= 0.237 Angle : 1.100 34.947 7630 Z= 0.420 Chirality : 0.120 2.248 853 Planarity : 0.004 0.043 921 Dihedral : 20.403 176.833 893 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.41 % Allowed : 14.31 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.04 (0.33), residues: 663 helix: 1.41 (0.28), residues: 329 sheet: -1.16 (0.44), residues: 134 loop : -1.35 (0.46), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 66 HIS 0.005 0.001 HIS A 94 PHE 0.010 0.001 PHE A 248 TYR 0.017 0.002 TYR A 311 ARG 0.001 0.000 ARG A 238 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 69 time to evaluate : 0.542 Fit side-chains REVERT: A 62 PHE cc_start: 0.8149 (t80) cc_final: 0.7924 (t80) REVERT: A 341 HIS cc_start: 0.7951 (OUTLIER) cc_final: 0.7018 (p-80) REVERT: A 452 TYR cc_start: 0.6755 (t80) cc_final: 0.6522 (t80) REVERT: B 217 CYS cc_start: 0.7065 (m) cc_final: 0.6830 (m) outliers start: 14 outliers final: 11 residues processed: 76 average time/residue: 0.2101 time to fit residues: 20.4046 Evaluate side-chains 80 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain B residue 214 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5612 Z= 0.167 Angle : 1.094 34.741 7630 Z= 0.410 Chirality : 0.118 2.198 853 Planarity : 0.004 0.042 921 Dihedral : 20.353 176.896 893 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.07 % Allowed : 15.34 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.27 (0.34), residues: 663 helix: 1.59 (0.28), residues: 329 sheet: -1.02 (0.44), residues: 134 loop : -1.25 (0.47), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 66 HIS 0.004 0.001 HIS L 111 PHE 0.008 0.001 PHE A 248 TYR 0.015 0.001 TYR L 52 ARG 0.002 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: A 62 PHE cc_start: 0.8082 (t80) cc_final: 0.7873 (t80) REVERT: A 112 MET cc_start: 0.5826 (tmm) cc_final: 0.5589 (ttm) REVERT: A 341 HIS cc_start: 0.7910 (OUTLIER) cc_final: 0.7022 (p-80) REVERT: A 452 TYR cc_start: 0.6633 (t80) cc_final: 0.6326 (t80) REVERT: B 217 CYS cc_start: 0.6922 (m) cc_final: 0.6659 (m) outliers start: 12 outliers final: 10 residues processed: 77 average time/residue: 0.1964 time to fit residues: 19.5066 Evaluate side-chains 78 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain B residue 214 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 5612 Z= 0.354 Angle : 1.138 35.338 7630 Z= 0.443 Chirality : 0.120 2.245 853 Planarity : 0.005 0.044 921 Dihedral : 20.478 177.240 893 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 2.41 % Allowed : 15.00 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.04 (0.33), residues: 663 helix: 1.25 (0.28), residues: 332 sheet: -0.99 (0.44), residues: 136 loop : -1.21 (0.48), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 74 HIS 0.007 0.001 HIS A 94 PHE 0.014 0.002 PHE A 215 TYR 0.022 0.002 TYR A 311 ARG 0.002 0.000 ARG A 238 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 67 time to evaluate : 0.556 Fit side-chains REVERT: A 341 HIS cc_start: 0.8003 (OUTLIER) cc_final: 0.7045 (p-80) REVERT: A 452 TYR cc_start: 0.6866 (t80) cc_final: 0.6443 (t80) REVERT: H 74 TYR cc_start: 0.7832 (OUTLIER) cc_final: 0.7190 (p90) REVERT: B 217 CYS cc_start: 0.7035 (m) cc_final: 0.6744 (m) outliers start: 14 outliers final: 10 residues processed: 77 average time/residue: 0.2193 time to fit residues: 21.2984 Evaluate side-chains 77 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 74 TYR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain B residue 214 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5612 Z= 0.184 Angle : 1.112 34.811 7630 Z= 0.421 Chirality : 0.118 2.195 853 Planarity : 0.004 0.042 921 Dihedral : 20.381 176.893 893 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.07 % Allowed : 16.03 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.32 (0.34), residues: 663 helix: 1.54 (0.28), residues: 330 sheet: -0.90 (0.44), residues: 134 loop : -1.16 (0.47), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 66 HIS 0.004 0.001 HIS L 111 PHE 0.008 0.001 PHE A 248 TYR 0.017 0.001 TYR L 52 ARG 0.003 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 69 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: A 112 MET cc_start: 0.5802 (tmm) cc_final: 0.5578 (ttm) REVERT: A 341 HIS cc_start: 0.7926 (OUTLIER) cc_final: 0.7035 (p-80) REVERT: B 217 CYS cc_start: 0.7019 (m) cc_final: 0.6745 (m) outliers start: 12 outliers final: 10 residues processed: 76 average time/residue: 0.2054 time to fit residues: 19.9520 Evaluate side-chains 78 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 214 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5612 Z= 0.247 Angle : 1.125 35.038 7630 Z= 0.430 Chirality : 0.119 2.204 853 Planarity : 0.004 0.044 921 Dihedral : 20.405 177.116 893 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.41 % Allowed : 16.03 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.29 (0.33), residues: 663 helix: 1.48 (0.28), residues: 330 sheet: -0.84 (0.44), residues: 134 loop : -1.16 (0.47), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 66 HIS 0.005 0.001 HIS A 94 PHE 0.010 0.001 PHE A 248 TYR 0.019 0.002 TYR L 52 ARG 0.002 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 67 time to evaluate : 0.608 Fit side-chains REVERT: A 112 MET cc_start: 0.5957 (tmm) cc_final: 0.5588 (ttm) REVERT: A 341 HIS cc_start: 0.7934 (OUTLIER) cc_final: 0.6948 (p-80) REVERT: L 24 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8414 (mmm) REVERT: B 217 CYS cc_start: 0.7004 (m) cc_final: 0.6712 (m) outliers start: 14 outliers final: 11 residues processed: 74 average time/residue: 0.2088 time to fit residues: 19.9061 Evaluate side-chains 78 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain L residue 24 MET Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 60 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 40 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 48 optimal weight: 0.0770 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 5612 Z= 0.158 Angle : 1.102 34.615 7630 Z= 0.414 Chirality : 0.118 2.173 853 Planarity : 0.004 0.042 921 Dihedral : 20.338 176.964 893 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.41 % Allowed : 16.21 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 (0.34), residues: 663 helix: 1.73 (0.28), residues: 329 sheet: -0.74 (0.44), residues: 134 loop : -1.10 (0.47), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 66 HIS 0.004 0.001 HIS L 111 PHE 0.007 0.001 PHE A 248 TYR 0.015 0.001 TYR L 52 ARG 0.003 0.000 ARG A 385 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 68 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: A 94 HIS cc_start: 0.6630 (OUTLIER) cc_final: 0.6363 (m90) REVERT: A 112 MET cc_start: 0.6061 (tmm) cc_final: 0.5643 (ttm) REVERT: A 341 HIS cc_start: 0.7939 (OUTLIER) cc_final: 0.7055 (p-80) REVERT: A 388 LEU cc_start: 0.7610 (tt) cc_final: 0.6997 (pp) REVERT: B 217 CYS cc_start: 0.7024 (m) cc_final: 0.6748 (m) outliers start: 14 outliers final: 10 residues processed: 76 average time/residue: 0.1907 time to fit residues: 18.7566 Evaluate side-chains 80 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 2.9990 chunk 21 optimal weight: 0.0570 chunk 53 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 overall best weight: 1.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.158802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.126091 restraints weight = 6246.079| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.01 r_work: 0.3309 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5612 Z= 0.264 Angle : 1.130 35.016 7630 Z= 0.433 Chirality : 0.119 2.198 853 Planarity : 0.004 0.043 921 Dihedral : 20.384 176.957 893 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.24 % Allowed : 16.55 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.38 (0.33), residues: 663 helix: 1.52 (0.28), residues: 330 sheet: -0.79 (0.44), residues: 135 loop : -1.06 (0.47), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 74 HIS 0.005 0.001 HIS A 94 PHE 0.011 0.001 PHE A 248 TYR 0.019 0.002 TYR L 52 ARG 0.003 0.000 ARG A 385 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1505.69 seconds wall clock time: 28 minutes 17.06 seconds (1697.06 seconds total)