Starting phenix.real_space_refine on Sun Mar 10 17:56:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsi_34998/03_2024/8hsi_34998_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsi_34998/03_2024/8hsi_34998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsi_34998/03_2024/8hsi_34998.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsi_34998/03_2024/8hsi_34998.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsi_34998/03_2024/8hsi_34998_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsi_34998/03_2024/8hsi_34998_trim_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.011 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 P 1 5.49 5 S 19 5.16 5 C 2352 2.51 5 N 541 2.21 5 O 603 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 371": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3516 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3314 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 12, 'TRANS': 392} Chain breaks: 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 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'CLR': 2, 'L9Q': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.80, per 1000 atoms: 0.80 Number of scatterers: 3516 At special positions: 0 Unit cell: (57.732, 60.279, 118.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 19 16.00 P 1 15.00 O 603 8.00 N 541 7.00 C 2352 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 128 " distance=2.02 Simple disulfide: pdb=" SG CYS A 89 " - pdb=" SG CYS A 431 " 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 B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG B 1 " - " ASN A 79 " " NAG C 1 " - " ASN A 62 " " NAG D 1 " - " ASN A 127 " Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 802.0 milliseconds 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 770 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 10 helices and 2 sheets defined 48.9% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 90 through 94 Processing helix chain 'A' and resid 98 through 107 removed outlier: 5.363A pdb=" N GLU A 102 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU A 105 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 250 Processing helix chain 'A' and resid 257 through 286 removed outlier: 3.759A pdb=" N TRP A 261 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE A 262 " --> pdb=" O GLN A 259 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS A 286 " --> pdb=" O ILE A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 316 removed outlier: 4.911A pdb=" N ILE A 295 " --> pdb=" O GLN A 291 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU A 296 " --> pdb=" O GLY A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 352 removed outlier: 3.659A pdb=" N LEU A 339 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY A 348 " --> pdb=" O GLY A 345 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N VAL A 349 " --> pdb=" O MET A 346 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU A 350 " --> pdb=" O GLU A 347 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 352 " --> pdb=" O VAL A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 392 Proline residue: A 366 - end of helix removed outlier: 3.672A pdb=" N LEU A 391 " --> pdb=" O LYS A 387 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 425 removed outlier: 3.908A pdb=" N LEU A 400 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 442 No H-bonds generated for 'chain 'A' and resid 440 through 442' Processing helix chain 'A' and resid 444 through 459 Processing sheet with id= A, first strand: chain 'A' and resid 41 through 44 Processing sheet with id= B, first strand: chain 'A' and resid 52 through 59 182 hydrogen bonds defined for protein. 417 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.86 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 500 1.31 - 1.44: 1056 1.44 - 1.57: 2022 1.57 - 1.70: 2 1.70 - 1.83: 31 Bond restraints: 3611 Sorted by residual: bond pdb=" C GLU A 72 " pdb=" N PRO A 73 " ideal model delta sigma weight residual 1.331 1.384 -0.053 1.31e-02 5.83e+03 1.66e+01 bond pdb=" C GLY A 292 " pdb=" N ALA A 293 " ideal model delta sigma weight residual 1.332 1.276 0.057 1.40e-02 5.10e+03 1.64e+01 bond pdb=" C31 L9Q A 601 " pdb=" O2 L9Q A 601 " ideal model delta sigma weight residual 1.330 1.402 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C11 L9Q A 601 " pdb=" O3 L9Q A 601 " ideal model delta sigma weight residual 1.327 1.397 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C4 CLR A 602 " pdb=" C5 CLR A 602 " ideal model delta sigma weight residual 1.506 1.440 0.066 2.00e-02 2.50e+03 1.08e+01 ... (remaining 3606 not shown) Histogram of bond angle deviations from ideal: 100.25 - 107.00: 98 107.00 - 113.75: 2085 113.75 - 120.50: 1372 120.50 - 127.24: 1295 127.24 - 133.99: 47 Bond angle restraints: 4897 Sorted by residual: angle pdb=" C PRO A 73 " pdb=" CA PRO A 73 " pdb=" CB PRO A 73 " ideal model delta sigma weight residual 110.98 123.69 -12.71 1.31e+00 5.83e-01 9.42e+01 angle pdb=" CA ILE A 46 " pdb=" C ILE A 46 " pdb=" N PRO A 47 " ideal model delta sigma weight residual 120.83 124.77 -3.94 6.10e-01 2.69e+00 4.18e+01 angle pdb=" CA ILE A 46 " pdb=" C ILE A 46 " pdb=" O ILE A 46 " ideal model delta sigma weight residual 118.69 114.65 4.04 6.70e-01 2.23e+00 3.63e+01 angle pdb=" N PRO A 73 " pdb=" CA PRO A 73 " pdb=" CB PRO A 73 " ideal model delta sigma weight residual 103.33 108.25 -4.92 9.30e-01 1.16e+00 2.80e+01 angle pdb=" CA PRO A 73 " pdb=" N PRO A 73 " pdb=" CD PRO A 73 " ideal model delta sigma weight residual 112.00 104.62 7.38 1.40e+00 5.10e-01 2.78e+01 ... (remaining 4892 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.28: 2094 22.28 - 44.56: 148 44.56 - 66.84: 29 66.84 - 89.12: 10 89.12 - 111.40: 21 Dihedral angle restraints: 2302 sinusoidal: 1113 harmonic: 1189 Sorted by residual: dihedral pdb=" C PRO A 73 " pdb=" N PRO A 73 " pdb=" CA PRO A 73 " pdb=" CB PRO A 73 " ideal model delta harmonic sigma weight residual -120.70 -135.81 15.11 0 2.50e+00 1.60e-01 3.65e+01 dihedral pdb=" CB CYS A 74 " pdb=" SG CYS A 74 " pdb=" SG CYS A 128 " pdb=" CB CYS A 128 " ideal model delta sinusoidal sigma weight residual -86.00 -36.80 -49.20 1 1.00e+01 1.00e-02 3.33e+01 dihedral pdb=" N PRO A 73 " pdb=" C PRO A 73 " pdb=" CA PRO A 73 " pdb=" CB PRO A 73 " ideal model delta harmonic sigma weight residual 115.10 127.29 -12.19 0 2.50e+00 1.60e-01 2.38e+01 ... (remaining 2299 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 560 0.110 - 0.221: 11 0.221 - 0.331: 3 0.331 - 0.441: 0 0.441 - 0.552: 1 Chirality restraints: 575 Sorted by residual: chirality pdb=" CA PRO A 73 " pdb=" N PRO A 73 " pdb=" C PRO A 73 " pdb=" CB PRO A 73 " both_signs ideal model delta sigma weight residual False 2.72 2.17 0.55 2.00e-01 2.50e+01 7.61e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 127 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.70 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 572 not shown) Planarity restraints: 567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 73 " 0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C PRO A 73 " -0.064 2.00e-02 2.50e+03 pdb=" O PRO A 73 " 0.023 2.00e-02 2.50e+03 pdb=" N CYS A 74 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 292 " -0.017 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C GLY A 292 " 0.062 2.00e-02 2.50e+03 pdb=" O GLY A 292 " -0.023 2.00e-02 2.50e+03 pdb=" N ALA A 293 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 293 " 0.015 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C ALA A 293 " -0.055 2.00e-02 2.50e+03 pdb=" O ALA A 293 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU A 294 " 0.019 2.00e-02 2.50e+03 ... (remaining 564 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 976 2.82 - 3.34: 3216 3.34 - 3.86: 5261 3.86 - 4.38: 5693 4.38 - 4.90: 10491 Nonbonded interactions: 25637 Sorted by model distance: nonbonded pdb=" O ASN A 465 " pdb=" NH1 ARG A 468 " model vdw 2.299 2.520 nonbonded pdb=" O SER A 472 " pdb=" OG SER A 472 " model vdw 2.300 2.440 nonbonded pdb=" CD GLU A 279 " pdb=" CB ALA A 293 " model vdw 2.405 3.690 nonbonded pdb=" O5 NAG D 1 " pdb=" O6 NAG D 1 " model vdw 2.453 2.432 nonbonded pdb=" N GLU A 217 " pdb=" OE1 GLU A 217 " model vdw 2.456 2.520 ... (remaining 25632 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 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 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: 6.690 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.720 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 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 : 0.005 0.072 3611 Z= 0.304 Angle : 0.848 12.714 4897 Z= 0.453 Chirality : 0.051 0.552 575 Planarity : 0.004 0.037 564 Dihedral : 19.622 111.397 1526 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.44), residues: 399 helix: 1.76 (0.38), residues: 206 sheet: 0.82 (0.64), residues: 65 loop : -3.00 (0.46), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 376 HIS 0.002 0.001 HIS A 43 PHE 0.026 0.001 PHE A 364 TYR 0.008 0.001 TYR A 104 ARG 0.005 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.395 Fit side-chains REVERT: A 112 ARG cc_start: 0.8856 (ptm-80) cc_final: 0.8337 (ttp80) REVERT: A 222 GLU cc_start: 0.6901 (tp30) cc_final: 0.6524 (tp30) REVERT: A 409 ILE cc_start: 0.8463 (tt) cc_final: 0.8209 (pt) REVERT: A 442 ASP cc_start: 0.8511 (m-30) cc_final: 0.8298 (m-30) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1466 time to fit residues: 8.4666 Evaluate side-chains 35 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 0.0970 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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: 0.7896 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3611 Z= 0.201 Angle : 0.603 7.959 4897 Z= 0.294 Chirality : 0.043 0.263 575 Planarity : 0.005 0.053 564 Dihedral : 16.691 89.445 757 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.51 % Allowed : 5.57 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.44), residues: 399 helix: 1.54 (0.39), residues: 207 sheet: 1.53 (0.64), residues: 61 loop : -2.82 (0.48), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 82 HIS 0.002 0.000 HIS A 171 PHE 0.008 0.001 PHE A 132 TYR 0.007 0.001 TYR A 401 ARG 0.003 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 35 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 112 ARG cc_start: 0.8891 (ptm-80) cc_final: 0.8400 (ttp80) REVERT: A 409 ILE cc_start: 0.8522 (tt) cc_final: 0.8310 (pt) REVERT: A 442 ASP cc_start: 0.8489 (m-30) cc_final: 0.8273 (m-30) outliers start: 9 outliers final: 8 residues processed: 41 average time/residue: 0.1297 time to fit residues: 7.0190 Evaluate side-chains 41 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 33 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 420 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 0.0050 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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: 0.7897 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3611 Z= 0.165 Angle : 0.561 6.895 4897 Z= 0.274 Chirality : 0.040 0.238 575 Planarity : 0.004 0.043 564 Dihedral : 13.496 82.797 757 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.39 % Allowed : 11.42 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.44), residues: 399 helix: 1.36 (0.39), residues: 207 sheet: 1.51 (0.64), residues: 63 loop : -2.85 (0.48), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 82 HIS 0.001 0.000 HIS A 143 PHE 0.007 0.001 PHE A 55 TYR 0.007 0.001 TYR A 83 ARG 0.004 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.410 Fit side-chains REVERT: A 112 ARG cc_start: 0.8890 (ptm-80) cc_final: 0.8417 (ttp80) REVERT: A 409 ILE cc_start: 0.8507 (tt) cc_final: 0.8298 (pt) outliers start: 5 outliers final: 5 residues processed: 38 average time/residue: 0.1398 time to fit residues: 7.0100 Evaluate side-chains 38 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 33 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 357 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 32 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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: 0.7938 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3611 Z= 0.214 Angle : 0.558 7.917 4897 Z= 0.275 Chirality : 0.040 0.258 575 Planarity : 0.004 0.039 564 Dihedral : 11.367 74.642 757 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.95 % Allowed : 12.81 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.45), residues: 399 helix: 1.30 (0.40), residues: 208 sheet: 1.72 (0.64), residues: 61 loop : -2.80 (0.48), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 82 HIS 0.001 0.001 HIS A 143 PHE 0.008 0.001 PHE A 60 TYR 0.008 0.001 TYR A 319 ARG 0.004 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 222 GLU cc_start: 0.8480 (pt0) cc_final: 0.8139 (pt0) REVERT: A 409 ILE cc_start: 0.8503 (tt) cc_final: 0.8269 (pt) outliers start: 7 outliers final: 7 residues processed: 38 average time/residue: 0.1452 time to fit residues: 7.2123 Evaluate side-chains 40 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 371 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 0.0470 chunk 22 optimal weight: 2.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- 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: 0.7948 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3611 Z= 0.220 Angle : 0.561 8.488 4897 Z= 0.276 Chirality : 0.040 0.244 575 Planarity : 0.004 0.038 564 Dihedral : 10.478 66.980 757 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.51 % Allowed : 13.65 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.45), residues: 399 helix: 1.19 (0.39), residues: 213 sheet: 1.80 (0.64), residues: 61 loop : -3.09 (0.49), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 82 HIS 0.001 0.000 HIS A 143 PHE 0.008 0.001 PHE A 132 TYR 0.007 0.001 TYR A 401 ARG 0.005 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 33 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 112 ARG cc_start: 0.8899 (ptm-80) cc_final: 0.8383 (ttp80) REVERT: A 409 ILE cc_start: 0.8512 (tt) cc_final: 0.8274 (pt) REVERT: A 466 ASN cc_start: 0.8373 (t0) cc_final: 0.8070 (t0) outliers start: 9 outliers final: 9 residues processed: 39 average time/residue: 0.1375 time to fit residues: 7.0562 Evaluate side-chains 41 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 32 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 371 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 32 optimal weight: 0.0470 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 37 optimal weight: 0.3980 chunk 4 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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: 0.7930 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3611 Z= 0.159 Angle : 0.536 8.405 4897 Z= 0.264 Chirality : 0.038 0.224 575 Planarity : 0.004 0.033 564 Dihedral : 9.666 62.654 757 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.79 % Allowed : 14.76 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.45), residues: 399 helix: 1.27 (0.40), residues: 212 sheet: 1.72 (0.64), residues: 63 loop : -3.17 (0.47), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 82 HIS 0.001 0.000 HIS A 143 PHE 0.010 0.001 PHE A 55 TYR 0.008 0.001 TYR A 83 ARG 0.006 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 33 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 112 ARG cc_start: 0.8902 (ptm-80) cc_final: 0.8397 (ttp80) REVERT: A 208 MET cc_start: 0.8905 (ttp) cc_final: 0.8565 (ttp) REVERT: A 409 ILE cc_start: 0.8491 (tt) cc_final: 0.8276 (pt) REVERT: A 466 ASN cc_start: 0.8397 (t0) cc_final: 0.8099 (t0) outliers start: 10 outliers final: 6 residues processed: 42 average time/residue: 0.1339 time to fit residues: 7.5762 Evaluate side-chains 39 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 352 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.0870 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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: 0.7940 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3611 Z= 0.182 Angle : 0.546 7.739 4897 Z= 0.273 Chirality : 0.039 0.187 575 Planarity : 0.004 0.034 564 Dihedral : 9.167 58.523 757 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.23 % Allowed : 15.32 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.45), residues: 399 helix: 1.28 (0.40), residues: 212 sheet: 1.78 (0.64), residues: 63 loop : -3.21 (0.46), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 82 HIS 0.001 0.000 HIS A 143 PHE 0.009 0.001 PHE A 55 TYR 0.007 0.001 TYR A 83 ARG 0.005 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 112 ARG cc_start: 0.8908 (ptm-80) cc_final: 0.8403 (ttp80) REVERT: A 279 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8242 (tp30) REVERT: A 409 ILE cc_start: 0.8496 (tt) cc_final: 0.8280 (pt) REVERT: A 466 ASN cc_start: 0.8273 (t0) cc_final: 0.7974 (t0) outliers start: 8 outliers final: 6 residues processed: 39 average time/residue: 0.1389 time to fit residues: 7.1599 Evaluate side-chains 38 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 352 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 11 optimal weight: 0.0970 chunk 32 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3611 Z= 0.183 Angle : 0.534 6.324 4897 Z= 0.268 Chirality : 0.038 0.146 575 Planarity : 0.004 0.034 564 Dihedral : 8.746 56.856 757 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.67 % Allowed : 16.16 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.45), residues: 399 helix: 1.29 (0.40), residues: 212 sheet: 1.76 (0.65), residues: 63 loop : -3.22 (0.47), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 82 HIS 0.001 0.001 HIS A 143 PHE 0.010 0.001 PHE A 364 TYR 0.007 0.001 TYR A 83 ARG 0.006 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 34 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 112 ARG cc_start: 0.8905 (ptm-80) cc_final: 0.8385 (ttp80) REVERT: A 279 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8234 (tp30) REVERT: A 409 ILE cc_start: 0.8497 (tt) cc_final: 0.8278 (pt) REVERT: A 466 ASN cc_start: 0.8418 (t0) cc_final: 0.8118 (t0) outliers start: 6 outliers final: 6 residues processed: 39 average time/residue: 0.1337 time to fit residues: 6.9027 Evaluate side-chains 39 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 352 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 0.0010 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 0.0970 chunk 25 optimal weight: 2.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- 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: 0.7930 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3611 Z= 0.159 Angle : 0.520 6.454 4897 Z= 0.263 Chirality : 0.038 0.141 575 Planarity : 0.004 0.033 564 Dihedral : 8.513 56.385 757 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.95 % Allowed : 15.88 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.45), residues: 399 helix: 1.33 (0.40), residues: 212 sheet: 1.74 (0.64), residues: 63 loop : -3.26 (0.46), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 82 HIS 0.002 0.000 HIS A 143 PHE 0.010 0.001 PHE A 55 TYR 0.007 0.001 TYR A 83 ARG 0.006 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 35 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 112 ARG cc_start: 0.8868 (ptm-80) cc_final: 0.8373 (ttp80) REVERT: A 279 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8239 (tp30) REVERT: A 466 ASN cc_start: 0.8223 (t0) cc_final: 0.7938 (t0) outliers start: 7 outliers final: 7 residues processed: 41 average time/residue: 0.1407 time to fit residues: 7.5650 Evaluate side-chains 41 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 34 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 0.0570 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 31 optimal weight: 0.4980 chunk 13 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 0.0170 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.4536 ------------------------------------------------------------------------------- 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: 0.7924 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3611 Z= 0.154 Angle : 0.506 5.815 4897 Z= 0.259 Chirality : 0.038 0.211 575 Planarity : 0.004 0.033 564 Dihedral : 8.420 56.020 757 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.23 % Allowed : 15.88 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.45), residues: 399 helix: 1.33 (0.40), residues: 212 sheet: 1.75 (0.64), residues: 63 loop : -3.25 (0.46), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 82 HIS 0.002 0.001 HIS A 143 PHE 0.010 0.001 PHE A 364 TYR 0.008 0.001 TYR A 319 ARG 0.010 0.000 ARG A 144 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 34 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.8863 (ptm-80) cc_final: 0.8360 (ttp80) REVERT: A 279 GLU cc_start: 0.8484 (tm-30) cc_final: 0.8235 (tp30) REVERT: A 466 ASN cc_start: 0.8301 (t0) cc_final: 0.8006 (t0) outliers start: 8 outliers final: 7 residues processed: 41 average time/residue: 0.1350 time to fit residues: 7.3131 Evaluate side-chains 40 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.105160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.073749 restraints weight = 5923.191| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.74 r_work: 0.2763 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3611 Z= 0.273 Angle : 0.563 5.985 4897 Z= 0.287 Chirality : 0.040 0.182 575 Planarity : 0.004 0.036 564 Dihedral : 8.688 57.110 757 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.95 % Allowed : 16.16 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.45), residues: 399 helix: 1.22 (0.39), residues: 213 sheet: 1.79 (0.64), residues: 63 loop : -3.27 (0.46), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 82 HIS 0.001 0.000 HIS A 171 PHE 0.008 0.001 PHE A 230 TYR 0.009 0.001 TYR A 401 ARG 0.011 0.001 ARG A 144 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1179.77 seconds wall clock time: 21 minutes 51.71 seconds (1311.71 seconds total)