Starting phenix.real_space_refine on Mon Mar 11 00:09:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p54_13194/03_2024/7p54_13194.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p54_13194/03_2024/7p54_13194.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p54_13194/03_2024/7p54_13194.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p54_13194/03_2024/7p54_13194.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p54_13194/03_2024/7p54_13194.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p54_13194/03_2024/7p54_13194.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 4030 2.51 5 N 986 2.21 5 O 1182 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6248 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3040 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 9, 'TRANS': 387} Chain breaks: 1 Chain: "B" Number of atoms: 3040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3040 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 9, 'TRANS': 387} Chain breaks: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.06, per 1000 atoms: 0.65 Number of scatterers: 6248 At special positions: 0 Unit cell: (93.744, 70.308, 128.898, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1182 8.00 N 986 7.00 C 4030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 274 " - pdb=" SG CYS A 382 " distance=2.03 Simple disulfide: pdb=" SG CYS A 300 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 274 " - pdb=" SG CYS B 382 " distance=2.02 Simple disulfide: pdb=" SG CYS B 300 " - pdb=" SG CYS B 367 " 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 601 " - " ASN A 283 " " NAG A 602 " - " ASN A 31 " " NAG B 601 " - " ASN B 283 " " NAG B 602 " - " ASN B 31 " " NAG C 1 " - " ASN A 352 " " NAG D 1 " - " ASN A 129 " " NAG E 1 " - " ASN B 352 " " NAG F 1 " - " ASN B 129 " Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.3 seconds 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1480 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 0 sheets defined 89.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 11 through 19 Processing helix chain 'A' and resid 38 through 72 Processing helix chain 'A' and resid 89 through 161 removed outlier: 4.269A pdb=" N LEU A 150 " --> pdb=" O MET A 146 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 160 " --> pdb=" O ARG A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 187 removed outlier: 3.744A pdb=" N LEU A 171 " --> pdb=" O TYR A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 237 Processing helix chain 'A' and resid 238 through 276 removed outlier: 3.560A pdb=" N SER A 244 " --> pdb=" O CYS A 240 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 285 Processing helix chain 'A' and resid 290 through 299 Processing helix chain 'A' and resid 308 through 337 removed outlier: 3.580A pdb=" N VAL A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Proline residue: A 335 - end of helix Processing helix chain 'A' and resid 341 through 365 Processing helix chain 'A' and resid 366 through 383 removed outlier: 4.482A pdb=" N LEU A 370 " --> pdb=" O ASP A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 409 Processing helix chain 'A' and resid 409 through 416 removed outlier: 3.614A pdb=" N ALA A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 19 Processing helix chain 'B' and resid 38 through 72 Processing helix chain 'B' and resid 89 through 161 removed outlier: 4.283A pdb=" N LEU B 150 " --> pdb=" O MET B 146 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE B 160 " --> pdb=" O ARG B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 187 removed outlier: 3.773A pdb=" N LEU B 171 " --> pdb=" O TYR B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 237 Processing helix chain 'B' and resid 239 through 276 removed outlier: 4.272A pdb=" N ALA B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 285 Processing helix chain 'B' and resid 290 through 300 Processing helix chain 'B' and resid 308 through 337 removed outlier: 3.597A pdb=" N VAL B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Proline residue: B 335 - end of helix Processing helix chain 'B' and resid 340 through 365 removed outlier: 3.772A pdb=" N LEU B 344 " --> pdb=" O ALA B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 383 removed outlier: 4.559A pdb=" N LEU B 370 " --> pdb=" O ASP B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 409 Processing helix chain 'B' and resid 409 through 416 removed outlier: 3.647A pdb=" N ALA B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) 581 hydrogen bonds defined for protein. 1743 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: 1.73 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1935 1.34 - 1.46: 1538 1.46 - 1.58: 2839 1.58 - 1.70: 0 1.70 - 1.82: 66 Bond restraints: 6378 Sorted by residual: bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.53e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.43e+00 bond pdb=" C1 NAG B 602 " pdb=" O5 NAG B 602 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" C1 NAG A 602 " pdb=" O5 NAG A 602 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.82e+00 bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.61e+00 ... (remaining 6373 not shown) Histogram of bond angle deviations from ideal: 98.93 - 105.95: 81 105.95 - 112.97: 3647 112.97 - 119.99: 2117 119.99 - 127.01: 2780 127.01 - 134.02: 67 Bond angle restraints: 8692 Sorted by residual: angle pdb=" C VAL B 23 " pdb=" N GLY B 24 " pdb=" CA GLY B 24 " ideal model delta sigma weight residual 121.44 117.03 4.41 1.45e+00 4.76e-01 9.25e+00 angle pdb=" N GLN A 325 " pdb=" CA GLN A 325 " pdb=" CB GLN A 325 " ideal model delta sigma weight residual 110.16 114.31 -4.15 1.48e+00 4.57e-01 7.87e+00 angle pdb=" N ARG B 368 " pdb=" CA ARG B 368 " pdb=" C ARG B 368 " ideal model delta sigma weight residual 111.11 114.34 -3.23 1.20e+00 6.94e-01 7.25e+00 angle pdb=" N GLY B 37 " pdb=" CA GLY B 37 " pdb=" C GLY B 37 " ideal model delta sigma weight residual 114.25 111.02 3.23 1.30e+00 5.92e-01 6.18e+00 angle pdb=" C CYS B 367 " pdb=" N ARG B 368 " pdb=" CA ARG B 368 " ideal model delta sigma weight residual 120.54 123.89 -3.35 1.35e+00 5.49e-01 6.16e+00 ... (remaining 8687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.06: 3460 16.06 - 32.12: 290 32.12 - 48.18: 91 48.18 - 64.23: 25 64.23 - 80.29: 8 Dihedral angle restraints: 3874 sinusoidal: 1570 harmonic: 2304 Sorted by residual: dihedral pdb=" CB CYS A 300 " pdb=" SG CYS A 300 " pdb=" SG CYS A 367 " pdb=" CB CYS A 367 " ideal model delta sinusoidal sigma weight residual -86.00 -162.49 76.49 1 1.00e+01 1.00e-02 7.36e+01 dihedral pdb=" CB CYS B 300 " pdb=" SG CYS B 300 " pdb=" SG CYS B 367 " pdb=" CB CYS B 367 " ideal model delta sinusoidal sigma weight residual -86.00 -141.61 55.61 1 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" CB CYS A 274 " pdb=" SG CYS A 274 " pdb=" SG CYS A 382 " pdb=" CB CYS A 382 " ideal model delta sinusoidal sigma weight residual 93.00 128.88 -35.88 1 1.00e+01 1.00e-02 1.82e+01 ... (remaining 3871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 985 0.063 - 0.126: 84 0.126 - 0.188: 1 0.188 - 0.251: 0 0.251 - 0.314: 2 Chirality restraints: 1072 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN B 129 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 129 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA GLN A 325 " pdb=" N GLN A 325 " pdb=" C GLN A 325 " pdb=" CB GLN A 325 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 1069 not shown) Planarity restraints: 1066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 20 " -0.055 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO A 21 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO A 21 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 21 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 20 " -0.053 5.00e-02 4.00e+02 8.04e-02 1.03e+01 pdb=" N PRO B 21 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO B 21 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 21 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 147 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.66e+00 pdb=" C LYS B 147 " 0.028 2.00e-02 2.50e+03 pdb=" O LYS B 147 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL B 148 " -0.009 2.00e-02 2.50e+03 ... (remaining 1063 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 737 2.74 - 3.28: 6440 3.28 - 3.82: 11254 3.82 - 4.36: 11217 4.36 - 4.90: 20634 Nonbonded interactions: 50282 Sorted by model distance: nonbonded pdb=" OD1 ASP A 278 " pdb=" OH TYR A 374 " model vdw 2.206 2.440 nonbonded pdb=" OD1 ASN B 111 " pdb=" NH1 ARG B 212 " model vdw 2.235 2.520 nonbonded pdb=" OD2 ASP A 38 " pdb=" OG SER A 40 " model vdw 2.237 2.440 nonbonded pdb=" O ILE B 281 " pdb=" OG1 THR B 285 " model vdw 2.240 2.440 nonbonded pdb=" OD1 ASN A 111 " pdb=" NH1 ARG A 212 " model vdw 2.243 2.520 ... (remaining 50277 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.960 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: 2.720 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 21.090 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6378 Z= 0.234 Angle : 0.553 6.891 8692 Z= 0.294 Chirality : 0.038 0.314 1072 Planarity : 0.005 0.083 1058 Dihedral : 13.935 80.293 2382 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.08 (0.29), residues: 786 helix: 3.32 (0.18), residues: 664 sheet: None (None), residues: 0 loop : -1.34 (0.49), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 213 HIS 0.002 0.001 HIS A 18 PHE 0.012 0.002 PHE B 395 TYR 0.010 0.001 TYR A 8 ARG 0.007 0.001 ARG B 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.686 Fit side-chains REVERT: A 16 TRP cc_start: 0.6870 (m100) cc_final: 0.6646 (m100) REVERT: A 207 TYR cc_start: 0.7718 (t80) cc_final: 0.7392 (t80) REVERT: A 213 TRP cc_start: 0.8415 (t60) cc_final: 0.7703 (t-100) REVERT: A 245 MET cc_start: 0.6533 (mmp) cc_final: 0.6259 (mmp) REVERT: A 353 SER cc_start: 0.8925 (t) cc_final: 0.8714 (t) REVERT: B 12 TRP cc_start: 0.8176 (p-90) cc_final: 0.7966 (p-90) REVERT: B 213 TRP cc_start: 0.8324 (t60) cc_final: 0.7643 (t-100) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.2024 time to fit residues: 35.2386 Evaluate side-chains 116 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS B 72 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6378 Z= 0.212 Angle : 0.487 4.607 8692 Z= 0.251 Chirality : 0.038 0.237 1072 Planarity : 0.004 0.053 1058 Dihedral : 7.499 59.772 1096 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.67 % Allowed : 8.79 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.26 (0.29), residues: 786 helix: 3.53 (0.18), residues: 666 sheet: None (None), residues: 0 loop : -1.95 (0.50), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 16 HIS 0.002 0.001 HIS A 18 PHE 0.017 0.002 PHE A 62 TYR 0.010 0.001 TYR A 8 ARG 0.005 0.001 ARG A 295 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 0.707 Fit side-chains REVERT: A 207 TYR cc_start: 0.7813 (t80) cc_final: 0.7444 (t80) REVERT: A 213 TRP cc_start: 0.8437 (t60) cc_final: 0.7673 (t-100) REVERT: A 332 PHE cc_start: 0.7826 (m-10) cc_final: 0.7619 (m-10) REVERT: A 353 SER cc_start: 0.8948 (t) cc_final: 0.8730 (t) REVERT: B 213 TRP cc_start: 0.8367 (t60) cc_final: 0.7592 (t-100) REVERT: B 283 ASN cc_start: 0.7901 (t0) cc_final: 0.7595 (t0) REVERT: B 322 MET cc_start: 0.8044 (mtp) cc_final: 0.7657 (mtp) REVERT: B 325 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.8088 (mp10) outliers start: 11 outliers final: 7 residues processed: 127 average time/residue: 0.1935 time to fit residues: 31.9999 Evaluate side-chains 126 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 118 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 0.0570 chunk 58 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- 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: 0.7338 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6378 Z= 0.191 Angle : 0.474 6.676 8692 Z= 0.239 Chirality : 0.037 0.223 1072 Planarity : 0.004 0.041 1058 Dihedral : 6.970 59.616 1096 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.67 % Allowed : 11.67 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.36 (0.29), residues: 786 helix: 3.62 (0.18), residues: 666 sheet: None (None), residues: 0 loop : -2.05 (0.49), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 16 HIS 0.002 0.001 HIS A 371 PHE 0.021 0.002 PHE A 62 TYR 0.011 0.001 TYR B 216 ARG 0.004 0.000 ARG A 26 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 121 time to evaluate : 0.651 Fit side-chains REVERT: A 207 TYR cc_start: 0.7861 (t80) cc_final: 0.7450 (t80) REVERT: A 213 TRP cc_start: 0.8443 (t60) cc_final: 0.7663 (t-100) REVERT: A 353 SER cc_start: 0.8944 (t) cc_final: 0.8720 (t) REVERT: B 213 TRP cc_start: 0.8452 (t60) cc_final: 0.7582 (t-100) REVERT: B 283 ASN cc_start: 0.7977 (t0) cc_final: 0.7644 (t0) REVERT: B 325 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.8079 (mp10) outliers start: 11 outliers final: 8 residues processed: 125 average time/residue: 0.2010 time to fit residues: 32.4618 Evaluate side-chains 129 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 120 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 325 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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: 0.7390 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6378 Z= 0.299 Angle : 0.529 6.186 8692 Z= 0.268 Chirality : 0.040 0.222 1072 Planarity : 0.004 0.038 1058 Dihedral : 6.704 59.567 1096 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.58 % Allowed : 15.00 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.02 (0.29), residues: 786 helix: 3.34 (0.18), residues: 674 sheet: None (None), residues: 0 loop : -2.23 (0.50), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 414 HIS 0.003 0.001 HIS A 22 PHE 0.026 0.002 PHE A 62 TYR 0.011 0.002 TYR B 216 ARG 0.004 0.001 ARG A 26 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 120 time to evaluate : 0.657 Fit side-chains REVERT: A 207 TYR cc_start: 0.8023 (t80) cc_final: 0.7512 (t80) REVERT: A 213 TRP cc_start: 0.8434 (t60) cc_final: 0.7653 (t-100) REVERT: A 353 SER cc_start: 0.9024 (t) cc_final: 0.8821 (t) REVERT: B 213 TRP cc_start: 0.8399 (t60) cc_final: 0.7552 (t-100) REVERT: B 272 ASP cc_start: 0.7886 (m-30) cc_final: 0.7483 (m-30) REVERT: B 283 ASN cc_start: 0.7954 (t0) cc_final: 0.7700 (t0) REVERT: B 325 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.8103 (mp10) outliers start: 17 outliers final: 12 residues processed: 128 average time/residue: 0.2068 time to fit residues: 33.9581 Evaluate side-chains 132 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 119 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 64 optimal weight: 0.2980 chunk 52 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 67 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 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: 0.7346 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6378 Z= 0.170 Angle : 0.454 6.863 8692 Z= 0.232 Chirality : 0.036 0.230 1072 Planarity : 0.003 0.034 1058 Dihedral : 6.421 59.998 1096 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.73 % Allowed : 16.52 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.39 (0.29), residues: 786 helix: 3.60 (0.18), residues: 676 sheet: None (None), residues: 0 loop : -2.30 (0.52), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 16 HIS 0.003 0.001 HIS A 371 PHE 0.026 0.002 PHE A 62 TYR 0.009 0.001 TYR A 216 ARG 0.003 0.000 ARG A 295 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 126 time to evaluate : 0.687 Fit side-chains REVERT: A 207 TYR cc_start: 0.7954 (t80) cc_final: 0.7489 (t80) REVERT: A 213 TRP cc_start: 0.8468 (t60) cc_final: 0.7612 (t-100) REVERT: A 283 ASN cc_start: 0.7798 (t0) cc_final: 0.7549 (t0) REVERT: A 325 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.6260 (mp10) REVERT: A 353 SER cc_start: 0.9000 (t) cc_final: 0.8789 (t) REVERT: B 213 TRP cc_start: 0.8505 (t60) cc_final: 0.7561 (t-100) REVERT: B 272 ASP cc_start: 0.7983 (m-30) cc_final: 0.7573 (m-30) REVERT: B 283 ASN cc_start: 0.8049 (t0) cc_final: 0.7801 (t0) REVERT: B 325 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.8058 (mp10) REVERT: B 353 SER cc_start: 0.9003 (t) cc_final: 0.8797 (t) outliers start: 18 outliers final: 14 residues processed: 135 average time/residue: 0.1912 time to fit residues: 33.3972 Evaluate side-chains 140 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 378 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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: 0.7398 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6378 Z= 0.287 Angle : 0.545 7.014 8692 Z= 0.272 Chirality : 0.040 0.223 1072 Planarity : 0.004 0.040 1058 Dihedral : 6.439 59.907 1096 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.64 % Allowed : 17.27 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.02 (0.29), residues: 786 helix: 3.33 (0.18), residues: 676 sheet: None (None), residues: 0 loop : -2.23 (0.51), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 414 HIS 0.003 0.001 HIS A 371 PHE 0.030 0.002 PHE B 62 TYR 0.013 0.002 TYR B 216 ARG 0.003 0.001 ARG A 295 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 0.594 Fit side-chains REVERT: A 207 TYR cc_start: 0.8075 (t80) cc_final: 0.7510 (t80) REVERT: A 213 TRP cc_start: 0.8408 (t60) cc_final: 0.7553 (t-100) REVERT: A 325 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.6173 (mp10) REVERT: A 337 PHE cc_start: 0.7894 (m-10) cc_final: 0.7606 (m-10) REVERT: B 26 ARG cc_start: 0.7499 (mpp80) cc_final: 0.7256 (mpp80) REVERT: B 213 TRP cc_start: 0.8447 (t60) cc_final: 0.7508 (t-100) REVERT: B 272 ASP cc_start: 0.8022 (m-30) cc_final: 0.7623 (m-30) REVERT: B 283 ASN cc_start: 0.8048 (t0) cc_final: 0.7814 (t0) REVERT: B 325 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.8072 (mp10) outliers start: 24 outliers final: 19 residues processed: 133 average time/residue: 0.1947 time to fit residues: 33.2887 Evaluate side-chains 139 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 378 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.7386 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6378 Z= 0.244 Angle : 0.504 7.232 8692 Z= 0.255 Chirality : 0.039 0.228 1072 Planarity : 0.004 0.034 1058 Dihedral : 6.366 58.991 1096 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.64 % Allowed : 19.09 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.09 (0.29), residues: 786 helix: 3.38 (0.18), residues: 676 sheet: None (None), residues: 0 loop : -2.24 (0.51), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 16 HIS 0.003 0.001 HIS A 371 PHE 0.030 0.002 PHE A 62 TYR 0.014 0.002 TYR B 216 ARG 0.003 0.000 ARG A 295 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 113 time to evaluate : 0.694 Fit side-chains REVERT: A 26 ARG cc_start: 0.7913 (mtm110) cc_final: 0.7670 (mpp80) REVERT: A 207 TYR cc_start: 0.8080 (t80) cc_final: 0.7526 (t80) REVERT: A 213 TRP cc_start: 0.8393 (t60) cc_final: 0.7538 (t-100) REVERT: A 283 ASN cc_start: 0.7939 (t0) cc_final: 0.7671 (t0) REVERT: A 325 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.6153 (mp10) REVERT: A 337 PHE cc_start: 0.7903 (m-10) cc_final: 0.7532 (m-10) REVERT: B 26 ARG cc_start: 0.7558 (mpp80) cc_final: 0.7334 (mpp80) REVERT: B 272 ASP cc_start: 0.7996 (m-30) cc_final: 0.7600 (m-30) REVERT: B 283 ASN cc_start: 0.8066 (t0) cc_final: 0.7825 (t0) REVERT: B 325 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.8060 (mp10) outliers start: 24 outliers final: 18 residues processed: 127 average time/residue: 0.1979 time to fit residues: 32.5493 Evaluate side-chains 131 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 111 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 378 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 65 optimal weight: 0.0970 chunk 70 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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: 0.7353 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6378 Z= 0.172 Angle : 0.465 7.545 8692 Z= 0.237 Chirality : 0.037 0.232 1072 Planarity : 0.003 0.034 1058 Dihedral : 6.201 58.593 1096 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.18 % Allowed : 19.39 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.43 (0.29), residues: 786 helix: 3.60 (0.18), residues: 678 sheet: None (None), residues: 0 loop : -2.20 (0.52), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 16 HIS 0.003 0.001 HIS A 371 PHE 0.030 0.002 PHE A 62 TYR 0.012 0.001 TYR B 216 ARG 0.004 0.000 ARG A 295 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 0.722 Fit side-chains REVERT: A 207 TYR cc_start: 0.7982 (t80) cc_final: 0.7442 (t80) REVERT: A 213 TRP cc_start: 0.8492 (t60) cc_final: 0.7616 (t-100) REVERT: A 283 ASN cc_start: 0.7952 (t0) cc_final: 0.7688 (t0) REVERT: A 325 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.6120 (mp10) REVERT: A 337 PHE cc_start: 0.7849 (m-10) cc_final: 0.7485 (m-10) REVERT: B 26 ARG cc_start: 0.7541 (mpp80) cc_final: 0.7318 (mpp80) REVERT: B 213 TRP cc_start: 0.8108 (t-100) cc_final: 0.7382 (t-100) REVERT: B 272 ASP cc_start: 0.7983 (m-30) cc_final: 0.7622 (m-30) REVERT: B 283 ASN cc_start: 0.8068 (t0) cc_final: 0.7820 (t0) REVERT: B 325 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.8055 (mp10) outliers start: 21 outliers final: 19 residues processed: 133 average time/residue: 0.1940 time to fit residues: 33.3244 Evaluate side-chains 139 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 378 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7365 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6378 Z= 0.203 Angle : 0.486 7.109 8692 Z= 0.248 Chirality : 0.038 0.229 1072 Planarity : 0.003 0.033 1058 Dihedral : 6.175 58.537 1096 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.03 % Allowed : 19.70 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.40 (0.29), residues: 786 helix: 3.58 (0.18), residues: 678 sheet: None (None), residues: 0 loop : -2.21 (0.52), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 16 HIS 0.003 0.001 HIS A 371 PHE 0.030 0.002 PHE A 62 TYR 0.011 0.001 TYR B 216 ARG 0.004 0.000 ARG A 295 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 0.672 Fit side-chains REVERT: A 26 ARG cc_start: 0.7908 (mtm110) cc_final: 0.7674 (mpp80) REVERT: A 207 TYR cc_start: 0.7976 (t80) cc_final: 0.7466 (t80) REVERT: A 213 TRP cc_start: 0.8507 (t60) cc_final: 0.7616 (t-100) REVERT: A 283 ASN cc_start: 0.7954 (t0) cc_final: 0.7682 (t0) REVERT: A 325 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.6119 (mp10) REVERT: A 337 PHE cc_start: 0.7863 (m-10) cc_final: 0.7452 (m-10) REVERT: B 213 TRP cc_start: 0.8133 (t-100) cc_final: 0.7411 (t-100) REVERT: B 283 ASN cc_start: 0.8017 (t0) cc_final: 0.7731 (t0) REVERT: B 325 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8039 (mp10) outliers start: 20 outliers final: 18 residues processed: 130 average time/residue: 0.1968 time to fit residues: 33.0259 Evaluate side-chains 137 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 378 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 65 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7355 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6378 Z= 0.182 Angle : 0.476 7.455 8692 Z= 0.243 Chirality : 0.037 0.229 1072 Planarity : 0.003 0.032 1058 Dihedral : 6.105 58.311 1096 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.03 % Allowed : 20.00 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.48 (0.29), residues: 786 helix: 3.63 (0.18), residues: 678 sheet: None (None), residues: 0 loop : -2.20 (0.52), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 16 HIS 0.003 0.001 HIS A 371 PHE 0.031 0.002 PHE B 62 TYR 0.011 0.001 TYR A 216 ARG 0.004 0.000 ARG A 295 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 0.665 Fit side-chains REVERT: A 26 ARG cc_start: 0.7876 (mtm110) cc_final: 0.7660 (mpp80) REVERT: A 207 TYR cc_start: 0.7941 (t80) cc_final: 0.7448 (t80) REVERT: A 213 TRP cc_start: 0.8490 (t60) cc_final: 0.7620 (t-100) REVERT: A 283 ASN cc_start: 0.7956 (t0) cc_final: 0.7678 (t0) REVERT: A 325 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.6105 (mp10) REVERT: A 337 PHE cc_start: 0.7868 (m-10) cc_final: 0.7512 (m-10) REVERT: B 164 ARG cc_start: 0.7346 (mtp-110) cc_final: 0.7096 (mtp-110) REVERT: B 213 TRP cc_start: 0.8112 (t-100) cc_final: 0.7412 (t-100) REVERT: B 283 ASN cc_start: 0.8011 (t0) cc_final: 0.7728 (t0) REVERT: B 325 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8024 (mp10) outliers start: 20 outliers final: 17 residues processed: 127 average time/residue: 0.1933 time to fit residues: 31.7325 Evaluate side-chains 134 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 378 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 3 optimal weight: 0.0570 chunk 44 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 41 optimal weight: 0.0470 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 = 0.3859 r_free = 0.3859 target = 0.158604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.130255 restraints weight = 6775.532| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.23 r_work: 0.3287 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6378 Z= 0.150 Angle : 0.454 7.181 8692 Z= 0.233 Chirality : 0.036 0.226 1072 Planarity : 0.003 0.033 1058 Dihedral : 5.960 57.913 1096 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.88 % Allowed : 21.06 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.66 (0.29), residues: 786 helix: 3.76 (0.18), residues: 678 sheet: None (None), residues: 0 loop : -2.13 (0.53), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 16 HIS 0.002 0.001 HIS A 371 PHE 0.030 0.002 PHE A 62 TYR 0.010 0.001 TYR B 216 ARG 0.006 0.000 ARG A 164 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1547.18 seconds wall clock time: 28 minutes 48.12 seconds (1728.12 seconds total)