Starting phenix.real_space_refine on Sun Mar 10 22:23:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urd_26709/03_2024/7urd_26709_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urd_26709/03_2024/7urd_26709.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urd_26709/03_2024/7urd_26709_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urd_26709/03_2024/7urd_26709_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urd_26709/03_2024/7urd_26709_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urd_26709/03_2024/7urd_26709.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urd_26709/03_2024/7urd_26709.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urd_26709/03_2024/7urd_26709_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urd_26709/03_2024/7urd_26709_updated.pdb" } resolution = 2.92 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= 0.007 sd= 0.087 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 3642 2.51 5 N 897 2.21 5 O 959 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 PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 27": "OD1" <-> "OD2" Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "A GLU 241": "OE1" <-> "OE2" Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 318": "NH1" <-> "NH2" Residue "A PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 47": "OE1" <-> "OE2" Residue "L PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 102": "OD1" <-> "OD2" Residue "L PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 92": "OD1" <-> "OD2" 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: 5534 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3449 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 14, 'TRANS': 417} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 158 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} 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: "A" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 172 Unusual residues: {' ZN': 1, 'AJP': 1, 'CLR': 2, 'O50': 1, 'OLA': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 9 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2833 SG CYS A 370 56.521 29.274 19.732 1.00108.35 S ATOM 2880 SG CYS A 376 55.636 28.723 23.034 1.00118.02 S ATOM 2908 SG CYS A 380 59.361 29.098 21.112 1.00127.74 S Time building chain proxies: 3.99, per 1000 atoms: 0.72 Number of scatterers: 5534 At special positions: 0 Unit cell: (98.77, 69.72, 93.79, 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 959 8.00 N 897 7.00 C 3642 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 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 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 506 " pdb="ZN ZN A 506 " - pdb=" SG CYS A 370 " pdb="ZN ZN A 506 " - pdb=" ND1 HIS A 382 " pdb="ZN ZN A 506 " - pdb=" SG CYS A 376 " pdb="ZN ZN A 506 " - pdb=" SG CYS A 380 " Number of angles added : 3 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 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: 22 helices and 7 sheets defined 46.5% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 6 through 27 removed outlier: 4.921A pdb=" N LEU A 14 " --> pdb=" O PHE A 10 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLN A 15 " --> pdb=" O GLN A 11 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N LEU A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) Proline residue: A 20 - end of helix Processing helix chain 'A' and resid 30 through 44 removed outlier: 3.842A 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: 4.758A pdb=" N LEU A 77 " --> pdb=" O TRP A 74 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU A 88 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 110 Processing helix chain 'A' and resid 117 through 143 removed outlier: 3.686A pdb=" N HIS A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG A 124 " --> pdb=" O TRP A 120 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLY A 125 " --> pdb=" O HIS A 121 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ALA A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A 129 " --> pdb=" O GLY A 125 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 173 through 181 removed outlier: 3.842A pdb=" N ALA A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 208 Processing helix chain 'A' and resid 235 through 263 removed outlier: 3.654A pdb=" N VAL A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 288 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 319 removed outlier: 5.869A pdb=" N ARG A 318 " --> pdb=" O LYS A 314 " (cutoff:3.500A) removed outlier: 5.794A 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 340 through 366 removed outlier: 3.610A pdb=" N ALA A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 412 removed outlier: 4.907A pdb=" N LEU A 411 " --> pdb=" O TYR A 407 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N PHE A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 435 Processing helix chain 'A' and resid 440 through 454 removed outlier: 3.713A pdb=" N PHE A 446 " --> pdb=" O HIS A 442 " (cutoff:3.500A) 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 helix chain 'H' and resid 107 through 109 No H-bonds generated for 'chain 'H' and resid 107 through 109' Processing sheet with id= A, first strand: chain 'B' and resid 202 through 206 Processing sheet with id= B, first strand: chain 'L' and resid 24 through 27 Processing sheet with id= C, first strand: chain 'L' and resid 30 through 33 removed outlier: 6.045A pdb=" N LYS L 123 " --> pdb=" O LEU L 31 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ALA L 33 " --> pdb=" O LYS L 123 " (cutoff:3.500A) removed outlier: 6.149A 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 54 through 58 Processing sheet with id= E, first strand: chain 'H' and resid 22 through 25 Processing sheet with id= F, first strand: chain 'H' and resid 29 through 31 Processing sheet with id= G, first strand: chain 'H' and resid 77 through 79 removed outlier: 6.634A pdb=" N TRP H 55 " --> pdb=" O ILE H 67 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ASN H 69 " --> pdb=" O MET H 53 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N MET H 53 " --> pdb=" O ASN H 69 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR H 127 " --> pdb=" O ARG H 117 " (cutoff:3.500A) 262 hydrogen bonds defined for protein. 720 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: 1.47 Time building geometry restraints manager: 2.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.19: 4 1.19 - 1.39: 2353 1.39 - 1.59: 3288 1.59 - 1.78: 10 1.78 - 1.98: 50 Bond restraints: 5705 Sorted by residual: bond pdb=" C07 AJP A 504 " pdb=" C08 AJP A 504 " ideal model delta sigma weight residual 1.550 1.980 -0.430 2.00e-02 2.50e+03 4.62e+02 bond pdb=" C01 AJP A 504 " pdb=" C02 AJP A 504 " ideal model delta sigma weight residual 1.521 1.947 -0.426 2.00e-02 2.50e+03 4.55e+02 bond pdb=" C08 AJP A 504 " pdb=" O09 AJP A 504 " ideal model delta sigma weight residual 1.410 0.998 0.412 2.00e-02 2.50e+03 4.24e+02 bond pdb=" C02 AJP A 504 " pdb=" C03 AJP A 504 " ideal model delta sigma weight residual 1.525 1.133 0.392 2.00e-02 2.50e+03 3.85e+02 bond pdb=" C05 AJP A 504 " pdb=" O09 AJP A 504 " ideal model delta sigma weight residual 1.407 1.784 -0.377 2.00e-02 2.50e+03 3.55e+02 ... (remaining 5700 not shown) Histogram of bond angle deviations from ideal: 87.28 - 98.09: 4 98.09 - 108.89: 429 108.89 - 119.69: 4468 119.69 - 130.49: 2826 130.49 - 141.29: 45 Bond angle restraints: 7772 Sorted by residual: angle pdb=" C06 AJP A 504 " pdb=" C07 AJP A 504 " pdb=" C12 AJP A 504 " ideal model delta sigma weight residual 120.30 141.29 -20.99 3.00e+00 1.11e-01 4.90e+01 angle pdb=" C11 AJP A 504 " pdb=" C12 AJP A 504 " pdb=" C81 AJP A 504 " ideal model delta sigma weight residual 114.35 98.09 16.26 3.00e+00 1.11e-01 2.94e+01 angle pdb=" C07 AJP A 504 " pdb=" C12 AJP A 504 " pdb=" C13 AJP A 504 " ideal model delta sigma weight residual 114.18 129.16 -14.98 3.00e+00 1.11e-01 2.49e+01 angle pdb=" C07 AJP A 504 " pdb=" C08 AJP A 504 " pdb=" C10 AJP A 504 " ideal model delta sigma weight residual 107.39 93.44 13.95 3.00e+00 1.11e-01 2.16e+01 angle pdb=" C PRO A 377 " pdb=" N PRO A 378 " pdb=" CA PRO A 378 " ideal model delta sigma weight residual 119.47 124.77 -5.30 1.16e+00 7.43e-01 2.09e+01 ... (remaining 7767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.55: 3317 34.55 - 69.10: 78 69.10 - 103.65: 34 103.65 - 138.20: 37 138.20 - 172.75: 14 Dihedral angle restraints: 3480 sinusoidal: 1518 harmonic: 1962 Sorted by residual: dihedral pdb=" CA TYR H 74 " pdb=" C TYR H 74 " pdb=" N VAL H 75 " pdb=" CA VAL H 75 " ideal model delta harmonic sigma weight residual -180.00 -152.22 -27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" C06 AJP A 504 " pdb=" C07 AJP A 504 " pdb=" C12 AJP A 504 " pdb=" C13 AJP A 504 " ideal model delta sinusoidal sigma weight residual 109.15 -63.60 172.75 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C12 AJP A 504 " pdb=" C10 AJP A 504 " pdb=" C11 AJP A 504 " pdb=" O82 AJP A 504 " ideal model delta sinusoidal sigma weight residual 287.38 117.68 169.70 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 3477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.107: 849 1.107 - 2.213: 0 2.213 - 3.320: 0 3.320 - 4.426: 1 4.426 - 5.533: 24 Chirality restraints: 874 Sorted by residual: chirality pdb=" C15 AJP A 504 " pdb=" C14 AJP A 504 " pdb=" C16 AJP A 504 " pdb=" C20 AJP A 504 " both_signs ideal model delta sigma weight residual False -2.42 3.11 -5.53 2.00e-01 2.50e+01 7.65e+02 chirality pdb=" C16 AJP A 504 " pdb=" C11 AJP A 504 " pdb=" C15 AJP A 504 " pdb=" C17 AJP A 504 " both_signs ideal model delta sigma weight residual False -2.70 2.76 -5.46 2.00e-01 2.50e+01 7.45e+02 chirality pdb=" C20 AJP A 504 " pdb=" C15 AJP A 504 " pdb=" C19 AJP A 504 " pdb=" C21 AJP A 504 " both_signs ideal model delta sigma weight residual False 2.96 -2.42 5.38 2.00e-01 2.50e+01 7.23e+02 ... (remaining 871 not shown) Planarity restraints: 924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 215 " -0.029 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO A 216 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 216 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 216 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 219 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO A 220 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 14 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.20e+00 pdb=" C LEU A 14 " 0.026 2.00e-02 2.50e+03 pdb=" O LEU A 14 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN A 15 " -0.009 2.00e-02 2.50e+03 ... (remaining 921 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 269 2.72 - 3.27: 5484 3.27 - 3.81: 9042 3.81 - 4.36: 11493 4.36 - 4.90: 19872 Nonbonded interactions: 46160 Sorted by model distance: nonbonded pdb=" OG SER A 242 " pdb=" OD1 ASP A 413 " model vdw 2.177 2.440 nonbonded pdb=" NH1 ARG A 360 " pdb=" O VAL A 371 " model vdw 2.196 2.520 nonbonded pdb=" OG SER H 26 " pdb=" OG SER H 40 " model vdw 2.251 2.440 nonbonded pdb=" OG SER L 27 " pdb=" OG1 THR L 42 " model vdw 2.266 2.440 nonbonded pdb=" OG SER A 79 " pdb=" OH TYR A 160 " model vdw 2.280 2.440 ... (remaining 46155 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.850 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 21.670 Find NCS groups from input model: 0.150 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:14.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 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 0.430 5705 Z= 1.237 Angle : 0.947 20.994 7772 Z= 0.410 Chirality : 0.833 5.533 874 Planarity : 0.004 0.043 924 Dihedral : 26.248 172.752 2211 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % 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: -2.44 (0.28), residues: 666 helix: -0.91 (0.25), residues: 324 sheet: -1.58 (0.42), residues: 129 loop : -2.50 (0.37), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 66 HIS 0.006 0.001 HIS A 94 PHE 0.018 0.001 PHE A 403 TYR 0.013 0.001 TYR A 83 ARG 0.002 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.7350 (mmt180) cc_final: 0.6938 (mtm180) REVERT: A 361 LYS cc_start: 0.7957 (tttt) cc_final: 0.7605 (ttpt) REVERT: A 432 HIS cc_start: 0.8143 (t-90) cc_final: 0.7735 (t70) REVERT: L 23 HIS cc_start: 0.8141 (m-70) cc_final: 0.7933 (m-70) REVERT: H 101 GLN cc_start: 0.8481 (tt0) cc_final: 0.8253 (tt0) REVERT: H 119 TYR cc_start: 0.6625 (t80) cc_final: 0.6393 (t80) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 1.1839 time to fit residues: 125.2839 Evaluate side-chains 73 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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: 0.6980 chunk 50 optimal weight: 0.0470 chunk 27 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 24 GLN A 66 HIS A 91 HIS A 94 HIS A 174 HIS A 247 HIS L 111 HIS H 52 ASN H 78 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5705 Z= 0.163 Angle : 1.088 32.393 7772 Z= 0.406 Chirality : 0.118 2.144 874 Planarity : 0.004 0.040 924 Dihedral : 20.336 179.935 1053 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.73 % Allowed : 9.53 % Favored : 88.73 % 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: -0.95 (0.32), residues: 666 helix: 0.47 (0.28), residues: 326 sheet: -1.25 (0.43), residues: 129 loop : -1.80 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 66 HIS 0.003 0.001 HIS A 94 PHE 0.014 0.001 PHE A 403 TYR 0.015 0.001 TYR H 74 ARG 0.004 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.7001 (tm-30) REVERT: A 109 MET cc_start: 0.6656 (mmt) cc_final: 0.6374 (mtm) REVERT: A 124 ARG cc_start: 0.7255 (OUTLIER) cc_final: 0.6960 (mtm-85) REVERT: A 142 ASP cc_start: 0.8125 (m-30) cc_final: 0.7815 (m-30) REVERT: A 154 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7510 (mt-10) REVERT: A 235 ARG cc_start: 0.7321 (mmt180) cc_final: 0.6933 (mtm180) REVERT: A 361 LYS cc_start: 0.7922 (tttt) cc_final: 0.7705 (ttpt) REVERT: A 375 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7766 (mtt-85) REVERT: A 432 HIS cc_start: 0.8103 (t-90) cc_final: 0.7759 (t70) REVERT: L 62 LYS cc_start: 0.8313 (mmtt) cc_final: 0.8073 (mmmt) REVERT: H 101 GLN cc_start: 0.8475 (tt0) cc_final: 0.8203 (tt0) REVERT: H 119 TYR cc_start: 0.6480 (t80) cc_final: 0.6271 (t80) outliers start: 10 outliers final: 1 residues processed: 88 average time/residue: 1.2662 time to fit residues: 116.3676 Evaluate side-chains 83 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 78 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 375 ARG 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: 0.5980 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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: 0.8181 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5705 Z= 0.222 Angle : 1.081 31.417 7772 Z= 0.406 Chirality : 0.118 2.113 874 Planarity : 0.004 0.040 924 Dihedral : 20.216 179.658 1053 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.73 % Allowed : 13.34 % Favored : 84.92 % 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 (0.33), residues: 666 helix: 0.92 (0.29), residues: 325 sheet: -0.90 (0.43), residues: 127 loop : -1.41 (0.43), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 66 HIS 0.002 0.001 HIS L 111 PHE 0.016 0.001 PHE A 403 TYR 0.015 0.001 TYR H 74 ARG 0.002 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.7446 (OUTLIER) cc_final: 0.7037 (tm-30) REVERT: A 109 MET cc_start: 0.6655 (mmt) cc_final: 0.6321 (mtm) REVERT: A 124 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.7037 (mtm-85) REVERT: A 142 ASP cc_start: 0.8147 (m-30) cc_final: 0.7836 (m-30) REVERT: A 154 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7554 (mt-10) REVERT: A 235 ARG cc_start: 0.7313 (mmt180) cc_final: 0.6954 (mtm180) REVERT: A 270 GLU cc_start: 0.8115 (pt0) cc_final: 0.7910 (pt0) REVERT: A 432 HIS cc_start: 0.8045 (t-90) cc_final: 0.7804 (t70) REVERT: H 101 GLN cc_start: 0.8487 (tt0) cc_final: 0.8218 (tt0) REVERT: H 119 TYR cc_start: 0.6483 (t80) cc_final: 0.6246 (t80) outliers start: 10 outliers final: 3 residues processed: 88 average time/residue: 1.2612 time to fit residues: 116.1064 Evaluate side-chains 84 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 285 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 6 optimal weight: 0.0870 chunk 28 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 17 optimal weight: 0.0770 chunk 53 optimal weight: 0.7980 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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: 0.8142 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5705 Z= 0.150 Angle : 1.063 31.582 7772 Z= 0.394 Chirality : 0.117 2.110 874 Planarity : 0.004 0.039 924 Dihedral : 20.125 179.742 1053 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.60 % Allowed : 13.52 % Favored : 83.88 % 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: 0.15 (0.33), residues: 666 helix: 1.31 (0.29), residues: 326 sheet: -0.77 (0.43), residues: 126 loop : -1.15 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 236 HIS 0.003 0.001 HIS A 336 PHE 0.012 0.001 PHE A 403 TYR 0.012 0.001 TYR H 74 ARG 0.002 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 89 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: A 7 GLN cc_start: 0.7566 (OUTLIER) cc_final: 0.7133 (tm-30) REVERT: A 109 MET cc_start: 0.6668 (mmt) cc_final: 0.6336 (mtm) REVERT: A 124 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.6846 (mtt-85) REVERT: A 142 ASP cc_start: 0.8086 (m-30) cc_final: 0.7824 (m-30) REVERT: A 154 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7543 (mt-10) REVERT: A 235 ARG cc_start: 0.7309 (mmt180) cc_final: 0.6968 (mtm180) REVERT: A 338 PHE cc_start: 0.7372 (t80) cc_final: 0.6577 (m-80) REVERT: A 375 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7823 (mtt-85) REVERT: A 432 HIS cc_start: 0.8058 (t-90) cc_final: 0.7854 (t70) REVERT: H 101 GLN cc_start: 0.8484 (tt0) cc_final: 0.8251 (tt0) REVERT: H 119 TYR cc_start: 0.6385 (t80) cc_final: 0.6152 (t80) outliers start: 15 outliers final: 2 residues processed: 98 average time/residue: 1.2333 time to fit residues: 126.5110 Evaluate side-chains 87 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 375 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 47 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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: 0.8185 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5705 Z= 0.242 Angle : 1.085 31.340 7772 Z= 0.408 Chirality : 0.118 2.101 874 Planarity : 0.004 0.039 924 Dihedral : 20.156 179.791 1053 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.91 % Allowed : 16.81 % Favored : 81.28 % 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: 0.21 (0.33), residues: 666 helix: 1.28 (0.29), residues: 325 sheet: -0.61 (0.44), residues: 126 loop : -1.06 (0.44), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 66 HIS 0.003 0.001 HIS A 94 PHE 0.016 0.001 PHE A 403 TYR 0.014 0.001 TYR A 83 ARG 0.002 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: A 7 GLN cc_start: 0.7571 (OUTLIER) cc_final: 0.7119 (tm-30) REVERT: A 109 MET cc_start: 0.6684 (mmt) cc_final: 0.6316 (mtm) REVERT: A 112 MET cc_start: 0.7858 (mtp) cc_final: 0.7498 (mtt) REVERT: A 124 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.7008 (mtm-85) REVERT: A 142 ASP cc_start: 0.8152 (m-30) cc_final: 0.7920 (m-30) REVERT: A 154 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7495 (mt-10) REVERT: A 235 ARG cc_start: 0.7345 (mmt180) cc_final: 0.6957 (mtm180) REVERT: A 432 HIS cc_start: 0.8105 (t-90) cc_final: 0.7830 (t70) REVERT: H 29 GLU cc_start: 0.6814 (mt-10) cc_final: 0.5981 (mm-30) REVERT: H 32 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.7860 (mtmm) REVERT: H 74 TYR cc_start: 0.7719 (OUTLIER) cc_final: 0.6838 (p90) REVERT: H 101 GLN cc_start: 0.8496 (tt0) cc_final: 0.8224 (tt0) outliers start: 11 outliers final: 2 residues processed: 86 average time/residue: 1.3193 time to fit residues: 118.5772 Evaluate side-chains 87 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain H residue 32 LYS Chi-restraints excluded: chain H residue 74 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 36 optimal weight: 0.0270 overall best weight: 0.6440 ------------------------------------------------------------------------------- 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: 0.8152 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 : 0.003 0.031 5705 Z= 0.171 Angle : 1.068 31.284 7772 Z= 0.398 Chirality : 0.118 2.103 874 Planarity : 0.004 0.040 924 Dihedral : 20.086 179.621 1053 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.91 % Allowed : 17.50 % Favored : 80.59 % 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: 0.44 (0.34), residues: 666 helix: 1.48 (0.30), residues: 326 sheet: -0.57 (0.44), residues: 128 loop : -0.93 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 74 HIS 0.003 0.001 HIS A 336 PHE 0.013 0.001 PHE A 403 TYR 0.012 0.001 TYR A 83 ARG 0.002 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 81 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: A 109 MET cc_start: 0.6680 (mmt) cc_final: 0.6294 (mtm) REVERT: A 112 MET cc_start: 0.7787 (mtp) cc_final: 0.7441 (mtt) REVERT: A 124 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6956 (mtm-85) REVERT: A 154 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7541 (mt-10) REVERT: A 235 ARG cc_start: 0.7335 (mmt180) cc_final: 0.6981 (mtm180) REVERT: A 432 HIS cc_start: 0.8087 (t-90) cc_final: 0.7828 (t70) REVERT: L 23 HIS cc_start: 0.7965 (m-70) cc_final: 0.7753 (m-70) REVERT: H 30 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8415 (tm) REVERT: H 39 MET cc_start: 0.8957 (ptp) cc_final: 0.8691 (ptp) REVERT: H 74 TYR cc_start: 0.7617 (OUTLIER) cc_final: 0.6759 (p90) REVERT: H 101 GLN cc_start: 0.8487 (tt0) cc_final: 0.8254 (tt0) outliers start: 11 outliers final: 4 residues processed: 86 average time/residue: 1.2678 time to fit residues: 114.1472 Evaluate side-chains 86 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 78 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 74 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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: 0.8170 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5705 Z= 0.216 Angle : 1.079 31.420 7772 Z= 0.404 Chirality : 0.118 2.101 874 Planarity : 0.004 0.040 924 Dihedral : 20.095 179.807 1053 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.43 % Allowed : 16.81 % Favored : 80.76 % 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: 0.43 (0.34), residues: 666 helix: 1.35 (0.29), residues: 331 sheet: -0.44 (0.44), residues: 128 loop : -0.87 (0.45), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 74 HIS 0.003 0.001 HIS A 336 PHE 0.015 0.001 PHE A 403 TYR 0.016 0.001 TYR H 51 ARG 0.001 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 78 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: A 109 MET cc_start: 0.6674 (mmt) cc_final: 0.6279 (mtm) REVERT: A 112 MET cc_start: 0.7789 (mtp) cc_final: 0.7428 (mtt) REVERT: A 124 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6901 (mtm-85) REVERT: A 154 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7576 (mt-10) REVERT: A 235 ARG cc_start: 0.7338 (mmt180) cc_final: 0.6971 (mtm180) REVERT: A 432 HIS cc_start: 0.8094 (t-90) cc_final: 0.7828 (t70) REVERT: L 23 HIS cc_start: 0.7951 (m-70) cc_final: 0.7750 (m-70) REVERT: H 30 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8326 (tm) REVERT: H 32 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7813 (mtmm) REVERT: H 39 MET cc_start: 0.9014 (ptp) cc_final: 0.8718 (ptp) REVERT: H 74 TYR cc_start: 0.7719 (OUTLIER) cc_final: 0.6868 (p90) outliers start: 14 outliers final: 5 residues processed: 83 average time/residue: 1.2515 time to fit residues: 108.7081 Evaluate side-chains 87 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 32 LYS Chi-restraints excluded: chain H residue 74 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 0.7980 chunk 40 optimal weight: 0.1980 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 50 optimal weight: 0.2980 chunk 57 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.8138 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5705 Z= 0.161 Angle : 1.069 31.317 7772 Z= 0.398 Chirality : 0.117 2.099 874 Planarity : 0.004 0.040 924 Dihedral : 20.058 179.705 1053 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.08 % Allowed : 17.68 % Favored : 80.24 % 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: 0.59 (0.34), residues: 666 helix: 1.47 (0.29), residues: 332 sheet: -0.40 (0.44), residues: 128 loop : -0.75 (0.45), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 74 HIS 0.003 0.001 HIS A 336 PHE 0.011 0.001 PHE A 403 TYR 0.017 0.001 TYR H 51 ARG 0.002 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: A 7 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.7235 (tm-30) REVERT: A 109 MET cc_start: 0.6677 (mmt) cc_final: 0.6290 (mtm) REVERT: A 112 MET cc_start: 0.7762 (mtp) cc_final: 0.7403 (mtt) REVERT: A 124 ARG cc_start: 0.7192 (OUTLIER) cc_final: 0.6890 (mtm-85) REVERT: A 154 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7559 (mt-10) REVERT: A 235 ARG cc_start: 0.7337 (mmt180) cc_final: 0.6992 (mtm180) REVERT: A 338 PHE cc_start: 0.7346 (t80) cc_final: 0.6531 (m-80) REVERT: A 375 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7736 (mtt-85) REVERT: A 432 HIS cc_start: 0.8111 (t-90) cc_final: 0.7852 (t70) REVERT: L 23 HIS cc_start: 0.7885 (m-70) cc_final: 0.7641 (m-70) REVERT: H 32 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7681 (mtmm) REVERT: H 74 TYR cc_start: 0.7721 (OUTLIER) cc_final: 0.6793 (p90) outliers start: 12 outliers final: 4 residues processed: 82 average time/residue: 1.3094 time to fit residues: 112.0789 Evaluate side-chains 82 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain H residue 32 LYS Chi-restraints excluded: chain H residue 74 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.8168 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5705 Z= 0.219 Angle : 1.083 31.513 7772 Z= 0.407 Chirality : 0.118 2.102 874 Planarity : 0.004 0.040 924 Dihedral : 20.074 179.626 1053 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.08 % Allowed : 18.02 % Favored : 79.90 % 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: 0.55 (0.34), residues: 666 helix: 1.38 (0.29), residues: 332 sheet: -0.36 (0.44), residues: 128 loop : -0.71 (0.45), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 74 HIS 0.003 0.001 HIS A 336 PHE 0.015 0.001 PHE A 403 TYR 0.017 0.001 TYR H 51 ARG 0.001 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: A 109 MET cc_start: 0.6681 (mmt) cc_final: 0.6277 (mtm) REVERT: A 112 MET cc_start: 0.7777 (mtp) cc_final: 0.7410 (mtt) REVERT: A 124 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6943 (mtm-85) REVERT: A 154 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7550 (mt-10) REVERT: A 235 ARG cc_start: 0.7346 (mmt180) cc_final: 0.6995 (mtm180) REVERT: A 432 HIS cc_start: 0.8102 (t-90) cc_final: 0.7822 (t70) REVERT: L 23 HIS cc_start: 0.7915 (m-70) cc_final: 0.7685 (m-70) REVERT: H 30 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7698 (mt) REVERT: H 32 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7853 (mtmm) REVERT: H 74 TYR cc_start: 0.7849 (OUTLIER) cc_final: 0.6838 (p90) outliers start: 12 outliers final: 4 residues processed: 81 average time/residue: 1.2131 time to fit residues: 102.8437 Evaluate side-chains 83 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 32 LYS Chi-restraints excluded: chain H residue 74 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 60 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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: 0.8172 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5705 Z= 0.234 Angle : 1.087 31.579 7772 Z= 0.410 Chirality : 0.118 2.102 874 Planarity : 0.004 0.040 924 Dihedral : 20.077 179.886 1053 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.56 % Allowed : 18.89 % Favored : 79.55 % 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: 0.49 (0.33), residues: 666 helix: 1.31 (0.29), residues: 331 sheet: -0.33 (0.45), residues: 128 loop : -0.73 (0.45), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 74 HIS 0.003 0.001 HIS A 336 PHE 0.016 0.001 PHE A 403 TYR 0.018 0.001 TYR H 51 ARG 0.002 0.000 ARG A 362 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: A 109 MET cc_start: 0.6703 (mmt) cc_final: 0.6287 (mtm) REVERT: A 112 MET cc_start: 0.7784 (mtp) cc_final: 0.7414 (mtt) REVERT: A 124 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.7013 (mtm180) REVERT: A 154 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7552 (mt-10) REVERT: A 235 ARG cc_start: 0.7359 (mmt180) cc_final: 0.6996 (mtm180) REVERT: A 432 HIS cc_start: 0.8118 (t-90) cc_final: 0.7791 (t70) REVERT: L 23 HIS cc_start: 0.7940 (m-70) cc_final: 0.7577 (m-70) REVERT: H 32 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.7900 (mtmm) REVERT: H 74 TYR cc_start: 0.7809 (OUTLIER) cc_final: 0.6845 (p90) outliers start: 9 outliers final: 3 residues processed: 78 average time/residue: 1.2934 time to fit residues: 105.3929 Evaluate side-chains 79 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain H residue 32 LYS Chi-restraints excluded: chain H residue 74 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 2 optimal weight: 0.0060 chunk 37 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 35 optimal weight: 0.0010 chunk 44 optimal weight: 2.9990 overall best weight: 0.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.130492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.094352 restraints weight = 6284.338| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.31 r_work: 0.2867 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5705 Z= 0.149 Angle : 1.066 31.323 7772 Z= 0.396 Chirality : 0.117 2.099 874 Planarity : 0.004 0.040 924 Dihedral : 20.032 179.683 1053 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.56 % Allowed : 19.58 % Favored : 78.86 % 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: 0.73 (0.34), residues: 666 helix: 1.52 (0.29), residues: 332 sheet: -0.23 (0.45), residues: 128 loop : -0.64 (0.46), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 74 HIS 0.003 0.001 HIS A 336 PHE 0.010 0.001 PHE A 403 TYR 0.018 0.001 TYR H 51 ARG 0.002 0.000 ARG A 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2591.82 seconds wall clock time: 46 minutes 34.15 seconds (2794.15 seconds total)