Starting phenix.real_space_refine on Sun Mar 10 19:51:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uae_26422/03_2024/7uae_26422.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uae_26422/03_2024/7uae_26422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uae_26422/03_2024/7uae_26422.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uae_26422/03_2024/7uae_26422.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uae_26422/03_2024/7uae_26422.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uae_26422/03_2024/7uae_26422.pdb" } resolution = 2.6 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= 0.003 sd= 0.044 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 1 6.06 5 S 21 5.16 5 C 2834 2.51 5 N 748 2.21 5 O 907 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A GLU 251": "OE1" <-> "OE2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A GLU 331": "OE1" <-> "OE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A ARG 458": "NH1" <-> "NH2" Residue "A ARG 483": "NH1" <-> "NH2" Residue "A ARG 504": "NH1" <-> "NH2" Residue "A GLU 514": "OE1" <-> "OE2" Residue "A ARG 546": "NH1" <-> "NH2" Residue "A ARG 549": "NH1" <-> "NH2" Residue "A ARG 578": "NH1" <-> "NH2" 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: 4513 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4313 Classifications: {'peptide': 535} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 515} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" 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: "C" 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: "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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 17 Unusual residues: {' CA': 2, ' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.41, per 1000 atoms: 0.76 Number of scatterers: 4513 At special positions: 0 Unit cell: (99.64, 81.62, 92.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Ca 2 19.99 S 21 16.00 O 907 8.00 N 748 7.00 C 2834 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 259 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 431 " distance=2.04 Simple disulfide: pdb=" SG CYS A 557 " - pdb=" SG CYS A 559 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " BETA1-6 " NAG F 1 " - " FUC F 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 704 " - " ASN A 539 " " NAG B 1 " - " ASN A 140 " " NAG C 1 " - " ASN A 258 " " NAG D 1 " - " ASN A 222 " " NAG E 1 " - " ASN A 440 " " NAG F 1 " - " ASN A 414 " Time building additional restraints: 2.18 Conformation dependent library (CDL) restraints added in 789.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 702 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 165 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 155 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 159 " 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 998 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 10 sheets defined 23.6% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 88 through 106 Processing helix chain 'A' and resid 149 through 162 Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 171 through 174 Processing helix chain 'A' and resid 180 through 183 Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 232 through 238 Processing helix chain 'A' and resid 246 through 258 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 440 through 448 removed outlier: 4.317A pdb=" N GLU A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 497 Processing helix chain 'A' and resid 516 through 520 Processing helix chain 'A' and resid 535 through 539 Processing helix chain 'A' and resid 546 through 551 Processing helix chain 'A' and resid 573 through 577 Processing helix chain 'A' and resid 597 through 600 Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 112 removed outlier: 7.977A pdb=" N PHE A 122 " --> pdb=" O PRO A 80 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE A 82 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE A 121 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 178 Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 269 Processing sheet with id=AA5, first strand: chain 'A' and resid 265 through 269 removed outlier: 5.726A pdb=" N LEU A 421 " --> pdb=" O LYS A 349 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LYS A 349 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ASP A 423 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE A 347 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 280 through 281 removed outlier: 6.790A pdb=" N LEU A 358 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N THR A 379 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL A 360 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 434 through 438 Processing sheet with id=AA8, first strand: chain 'A' and resid 454 through 455 Processing sheet with id=AA9, first strand: chain 'A' and resid 454 through 455 removed outlier: 3.951A pdb=" N GLY A 466 " --> pdb=" O CYS A 489 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU A 482 " --> pdb=" O GLY A 569 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 552 through 553 158 hydrogen bonds defined for protein. 354 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: 1.55 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1084 1.33 - 1.45: 1057 1.45 - 1.57: 2449 1.57 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 4620 Sorted by residual: bond pdb=" CZ ARG A 169 " pdb=" NH2 ARG A 169 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 1.01e+01 bond pdb=" CZ ARG A 172 " pdb=" NH2 ARG A 172 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 9.92e+00 bond pdb=" N VAL A 371 " pdb=" CA VAL A 371 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.71e+00 bond pdb=" CZ ARG A 518 " pdb=" NH2 ARG A 518 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.58e+00 bond pdb=" CZ ARG A 103 " pdb=" NH2 ARG A 103 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.47e+00 ... (remaining 4615 not shown) Histogram of bond angle deviations from ideal: 97.33 - 104.87: 70 104.87 - 112.40: 2083 112.40 - 119.94: 1989 119.94 - 127.47: 2086 127.47 - 135.01: 43 Bond angle restraints: 6271 Sorted by residual: angle pdb=" CA PHE A 590 " pdb=" CB PHE A 590 " pdb=" CG PHE A 590 " ideal model delta sigma weight residual 113.80 118.92 -5.12 1.00e+00 1.00e+00 2.62e+01 angle pdb=" CA ASP A 564 " pdb=" CB ASP A 564 " pdb=" CG ASP A 564 " ideal model delta sigma weight residual 112.60 117.67 -5.07 1.00e+00 1.00e+00 2.57e+01 angle pdb=" N TYR A 113 " pdb=" CA TYR A 113 " pdb=" C TYR A 113 " ideal model delta sigma weight residual 111.07 116.26 -5.19 1.07e+00 8.73e-01 2.35e+01 angle pdb=" CB HIS A 573 " pdb=" CG HIS A 573 " pdb=" CD2 HIS A 573 " ideal model delta sigma weight residual 131.20 124.97 6.23 1.30e+00 5.92e-01 2.30e+01 angle pdb=" OE1 GLN A 345 " pdb=" CD GLN A 345 " pdb=" NE2 GLN A 345 " ideal model delta sigma weight residual 122.60 117.87 4.73 1.00e+00 1.00e+00 2.23e+01 ... (remaining 6266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.24: 2740 21.24 - 42.48: 119 42.48 - 63.72: 19 63.72 - 84.96: 23 84.96 - 106.19: 13 Dihedral angle restraints: 2914 sinusoidal: 1359 harmonic: 1555 Sorted by residual: dihedral pdb=" CB CYS A 128 " pdb=" SG CYS A 128 " pdb=" SG CYS A 147 " pdb=" CB CYS A 147 " ideal model delta sinusoidal sigma weight residual 93.00 -176.94 -90.06 1 1.00e+01 1.00e-02 9.61e+01 dihedral pdb=" CB CYS A 557 " pdb=" SG CYS A 557 " pdb=" SG CYS A 559 " pdb=" CB CYS A 559 " ideal model delta sinusoidal sigma weight residual -86.00 -139.17 53.17 1 1.00e+01 1.00e-02 3.84e+01 dihedral pdb=" CA TRP A 567 " pdb=" C TRP A 567 " pdb=" N SER A 568 " pdb=" CA SER A 568 " ideal model delta harmonic sigma weight residual 180.00 150.29 29.71 0 5.00e+00 4.00e-02 3.53e+01 ... (remaining 2911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 398 0.079 - 0.157: 236 0.157 - 0.236: 62 0.236 - 0.314: 14 0.314 - 0.393: 4 Chirality restraints: 714 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-02 2.50e+03 1.93e+02 chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.44e+01 chirality pdb=" C1 FUC F 4 " pdb=" O6 NAG F 1 " pdb=" C2 FUC F 4 " pdb=" O5 FUC F 4 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.73e+01 ... (remaining 711 not shown) Planarity restraints: 803 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " -0.314 2.00e-02 2.50e+03 2.72e-01 9.25e+02 pdb=" C7 NAG C 1 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " -0.027 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " 0.474 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " -0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.205 2.00e-02 2.50e+03 1.68e-01 3.55e+02 pdb=" C7 NAG D 1 " 0.056 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.148 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.273 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 704 " 0.183 2.00e-02 2.50e+03 1.51e-01 2.85e+02 pdb=" C7 NAG A 704 " -0.051 2.00e-02 2.50e+03 pdb=" C8 NAG A 704 " 0.134 2.00e-02 2.50e+03 pdb=" N2 NAG A 704 " -0.245 2.00e-02 2.50e+03 pdb=" O7 NAG A 704 " -0.021 2.00e-02 2.50e+03 ... (remaining 800 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 823 2.81 - 3.33: 4208 3.33 - 3.85: 7306 3.85 - 4.38: 9238 4.38 - 4.90: 15059 Nonbonded interactions: 36634 Sorted by model distance: nonbonded pdb=" OD1 ASP A 288 " pdb="CA CA A 701 " model vdw 2.282 2.510 nonbonded pdb=" OE2 GLU A 272 " pdb="CA CA A 703 " model vdw 2.302 2.510 nonbonded pdb=" O TYR A 313 " pdb="CA CA A 703 " model vdw 2.329 2.510 nonbonded pdb=" OD1 ASP A 285 " pdb="CA CA A 701 " model vdw 2.329 2.510 nonbonded pdb=" OD2 ASP A 285 " pdb="CA CA A 701 " model vdw 2.379 2.510 ... (remaining 36629 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' } ncs_group { reference = chain 'D' selection = chain 'E' } 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: 0.580 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: 2.550 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.720 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:12.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 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 : 0.012 0.041 4620 Z= 0.754 Angle : 1.756 9.028 6271 Z= 1.171 Chirality : 0.102 0.393 714 Planarity : 0.020 0.272 797 Dihedral : 16.442 106.193 1901 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 0.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 10.53 % 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 (0.34), residues: 533 helix: -0.97 (0.58), residues: 62 sheet: 0.51 (0.43), residues: 131 loop : -0.13 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.016 TRP A 544 HIS 0.012 0.003 HIS A 573 PHE 0.067 0.011 PHE A 593 TYR 0.104 0.020 TYR A 313 ARG 0.009 0.001 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 107 CYS cc_start: 0.6218 (p) cc_final: 0.5910 (p) REVERT: A 207 ASP cc_start: 0.7669 (t0) cc_final: 0.7190 (t0) REVERT: A 212 MET cc_start: 0.8801 (mmm) cc_final: 0.8479 (mmm) REVERT: A 251 GLU cc_start: 0.7570 (tt0) cc_final: 0.7321 (tt0) REVERT: A 272 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7292 (mp0) REVERT: A 423 ASP cc_start: 0.7931 (m-30) cc_final: 0.7573 (m-30) REVERT: A 447 ASN cc_start: 0.8660 (m-40) cc_final: 0.8232 (m-40) REVERT: A 512 ASP cc_start: 0.8064 (t0) cc_final: 0.7857 (t0) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 1.2749 time to fit residues: 155.6776 Evaluate side-chains 79 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 461 ASN A 474 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4620 Z= 0.231 Angle : 0.667 9.604 6271 Z= 0.347 Chirality : 0.047 0.208 714 Planarity : 0.004 0.025 797 Dihedral : 11.776 66.213 890 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.47 % Allowed : 11.76 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.02 (0.34), residues: 533 helix: -0.22 (0.61), residues: 69 sheet: 0.49 (0.43), residues: 136 loop : -0.07 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 361 HIS 0.009 0.002 HIS A 155 PHE 0.017 0.002 PHE A 245 TYR 0.010 0.001 TYR A 175 ARG 0.004 0.001 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 196 ASP cc_start: 0.8311 (p0) cc_final: 0.8108 (p0) REVERT: A 207 ASP cc_start: 0.7781 (t0) cc_final: 0.7416 (t0) REVERT: A 397 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7077 (mm-30) REVERT: A 411 ASP cc_start: 0.7805 (t0) cc_final: 0.7568 (t0) REVERT: A 415 SER cc_start: 0.8740 (t) cc_final: 0.8500 (p) REVERT: A 423 ASP cc_start: 0.8089 (m-30) cc_final: 0.7778 (m-30) REVERT: A 494 ASP cc_start: 0.8009 (m-30) cc_final: 0.7797 (m-30) REVERT: A 512 ASP cc_start: 0.7997 (t0) cc_final: 0.7746 (t0) outliers start: 7 outliers final: 4 residues processed: 87 average time/residue: 1.1422 time to fit residues: 103.4648 Evaluate side-chains 79 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 398 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4620 Z= 0.217 Angle : 0.587 9.333 6271 Z= 0.303 Chirality : 0.045 0.196 714 Planarity : 0.003 0.028 797 Dihedral : 6.992 32.337 890 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.36 % Allowed : 12.39 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.13 (0.35), residues: 533 helix: 0.22 (0.64), residues: 69 sheet: 0.43 (0.43), residues: 140 loop : -0.01 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 361 HIS 0.007 0.001 HIS A 155 PHE 0.013 0.001 PHE A 593 TYR 0.016 0.001 TYR A 97 ARG 0.002 0.000 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 76 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: A 207 ASP cc_start: 0.7764 (t0) cc_final: 0.7383 (t0) REVERT: A 251 GLU cc_start: 0.7681 (tt0) cc_final: 0.7433 (tt0) REVERT: A 397 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7081 (mm-30) REVERT: A 411 ASP cc_start: 0.7974 (t0) cc_final: 0.7587 (t0) REVERT: A 415 SER cc_start: 0.8805 (t) cc_final: 0.8462 (p) REVERT: A 423 ASP cc_start: 0.8084 (m-30) cc_final: 0.7789 (m-30) REVERT: A 512 ASP cc_start: 0.7997 (t0) cc_final: 0.7754 (t0) REVERT: A 525 MET cc_start: 0.8169 (mmm) cc_final: 0.7803 (mtm) REVERT: A 585 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7171 (t0) outliers start: 16 outliers final: 5 residues processed: 83 average time/residue: 1.0962 time to fit residues: 94.9200 Evaluate side-chains 83 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 585 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 0.0030 chunk 36 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 4620 Z= 0.412 Angle : 0.634 10.231 6271 Z= 0.329 Chirality : 0.047 0.202 714 Planarity : 0.004 0.031 797 Dihedral : 5.757 30.554 890 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.94 % Allowed : 14.71 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 (0.35), residues: 533 helix: 0.33 (0.65), residues: 69 sheet: 0.39 (0.42), residues: 148 loop : -0.26 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 361 HIS 0.008 0.002 HIS A 155 PHE 0.013 0.002 PHE A 486 TYR 0.018 0.002 TYR A 97 ARG 0.004 0.001 ARG A 578 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 77 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: A 188 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.8062 (pm20) REVERT: A 192 ASP cc_start: 0.7877 (m-30) cc_final: 0.7664 (m-30) REVERT: A 207 ASP cc_start: 0.7815 (t0) cc_final: 0.7453 (t0) REVERT: A 227 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8431 (p) REVERT: A 251 GLU cc_start: 0.7691 (tt0) cc_final: 0.7457 (tt0) REVERT: A 397 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7000 (mm-30) REVERT: A 411 ASP cc_start: 0.8063 (t0) cc_final: 0.7635 (t0) REVERT: A 483 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8051 (ttt-90) REVERT: A 512 ASP cc_start: 0.8023 (t0) cc_final: 0.7792 (t0) REVERT: A 525 MET cc_start: 0.8215 (mmm) cc_final: 0.7794 (mtm) REVERT: A 585 ASP cc_start: 0.7639 (t70) cc_final: 0.7223 (t0) outliers start: 14 outliers final: 5 residues processed: 84 average time/residue: 1.1650 time to fit residues: 101.8259 Evaluate side-chains 78 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 483 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 HIS A 455 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4620 Z= 0.243 Angle : 0.574 10.987 6271 Z= 0.297 Chirality : 0.044 0.217 714 Planarity : 0.003 0.030 797 Dihedral : 5.210 29.310 890 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.52 % Allowed : 15.55 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.36), residues: 533 helix: 0.48 (0.65), residues: 69 sheet: 0.45 (0.43), residues: 148 loop : -0.25 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 361 HIS 0.007 0.001 HIS A 155 PHE 0.012 0.001 PHE A 527 TYR 0.016 0.001 TYR A 97 ARG 0.002 0.000 ARG A 578 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: A 192 ASP cc_start: 0.7872 (m-30) cc_final: 0.7658 (m-30) REVERT: A 201 ASP cc_start: 0.8066 (p0) cc_final: 0.7824 (p0) REVERT: A 207 ASP cc_start: 0.7794 (t0) cc_final: 0.7424 (t0) REVERT: A 251 GLU cc_start: 0.7675 (tt0) cc_final: 0.7436 (tt0) REVERT: A 284 ARG cc_start: 0.3964 (ttt180) cc_final: 0.1591 (tmt170) REVERT: A 397 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7080 (mm-30) REVERT: A 411 ASP cc_start: 0.8068 (t0) cc_final: 0.7648 (t0) REVERT: A 483 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8038 (ttt-90) REVERT: A 512 ASP cc_start: 0.8003 (t0) cc_final: 0.7745 (t0) REVERT: A 525 MET cc_start: 0.8172 (mmm) cc_final: 0.7794 (mtm) REVERT: A 585 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.7196 (t0) outliers start: 12 outliers final: 4 residues processed: 79 average time/residue: 1.0842 time to fit residues: 89.3480 Evaluate side-chains 76 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 483 ARG Chi-restraints excluded: chain A residue 585 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 0.7980 chunk 30 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 5 optimal weight: 0.4980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4620 Z= 0.260 Angle : 0.567 10.951 6271 Z= 0.293 Chirality : 0.045 0.214 714 Planarity : 0.003 0.030 797 Dihedral : 4.980 30.576 890 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.10 % Allowed : 16.39 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.08 (0.36), residues: 533 helix: 0.75 (0.66), residues: 66 sheet: 0.51 (0.44), residues: 148 loop : -0.26 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 361 HIS 0.007 0.001 HIS A 155 PHE 0.012 0.001 PHE A 527 TYR 0.018 0.001 TYR A 97 ARG 0.002 0.000 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 69 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 192 ASP cc_start: 0.7888 (m-30) cc_final: 0.7684 (m-30) REVERT: A 201 ASP cc_start: 0.8108 (p0) cc_final: 0.7851 (p0) REVERT: A 207 ASP cc_start: 0.7796 (t0) cc_final: 0.7435 (t0) REVERT: A 209 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7568 (tt0) REVERT: A 251 GLU cc_start: 0.7681 (tt0) cc_final: 0.7433 (tt0) REVERT: A 284 ARG cc_start: 0.3633 (ttt180) cc_final: 0.1243 (ppt170) REVERT: A 397 GLU cc_start: 0.7456 (mm-30) cc_final: 0.6889 (mm-30) REVERT: A 411 ASP cc_start: 0.8037 (t0) cc_final: 0.7616 (t0) REVERT: A 512 ASP cc_start: 0.8001 (t0) cc_final: 0.7733 (t0) REVERT: A 525 MET cc_start: 0.8188 (mmm) cc_final: 0.7817 (mtm) REVERT: A 565 LEU cc_start: 0.8943 (tp) cc_final: 0.8732 (tt) REVERT: A 585 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.7187 (t0) outliers start: 10 outliers final: 5 residues processed: 74 average time/residue: 1.0589 time to fit residues: 81.9004 Evaluate side-chains 75 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 585 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4620 Z= 0.258 Angle : 0.579 12.337 6271 Z= 0.299 Chirality : 0.045 0.195 714 Planarity : 0.003 0.029 797 Dihedral : 4.900 31.023 890 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.31 % Allowed : 16.60 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.08 (0.36), residues: 533 helix: 0.80 (0.67), residues: 66 sheet: 0.54 (0.44), residues: 148 loop : -0.30 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 129 HIS 0.007 0.001 HIS A 155 PHE 0.012 0.001 PHE A 527 TYR 0.021 0.001 TYR A 97 ARG 0.002 0.000 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 ASP cc_start: 0.7888 (m-30) cc_final: 0.7677 (m-30) REVERT: A 201 ASP cc_start: 0.8115 (p0) cc_final: 0.7841 (p0) REVERT: A 207 ASP cc_start: 0.7806 (t0) cc_final: 0.7436 (t0) REVERT: A 251 GLU cc_start: 0.7677 (tt0) cc_final: 0.7428 (tt0) REVERT: A 284 ARG cc_start: 0.3682 (ttt180) cc_final: 0.1183 (tmt170) REVERT: A 397 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7017 (mm-30) REVERT: A 411 ASP cc_start: 0.8045 (t0) cc_final: 0.7623 (t0) REVERT: A 463 GLU cc_start: 0.5084 (tp30) cc_final: 0.4705 (tp30) REVERT: A 483 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7982 (ttt-90) REVERT: A 501 VAL cc_start: 0.8249 (OUTLIER) cc_final: 0.7963 (t) REVERT: A 512 ASP cc_start: 0.7996 (t0) cc_final: 0.7731 (t0) REVERT: A 525 MET cc_start: 0.8181 (mmm) cc_final: 0.7817 (mtm) REVERT: A 565 LEU cc_start: 0.8943 (tp) cc_final: 0.8716 (tt) REVERT: A 585 ASP cc_start: 0.7613 (OUTLIER) cc_final: 0.7203 (t0) outliers start: 11 outliers final: 6 residues processed: 79 average time/residue: 1.1154 time to fit residues: 91.8024 Evaluate side-chains 79 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 483 ARG Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 585 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 4 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4620 Z= 0.202 Angle : 0.568 7.998 6271 Z= 0.298 Chirality : 0.044 0.176 714 Planarity : 0.003 0.030 797 Dihedral : 4.741 30.479 890 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.73 % Allowed : 17.02 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 (0.36), residues: 533 helix: 0.87 (0.67), residues: 66 sheet: 0.55 (0.44), residues: 148 loop : -0.28 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 129 HIS 0.007 0.001 HIS A 155 PHE 0.012 0.001 PHE A 527 TYR 0.007 0.001 TYR A 257 ARG 0.002 0.000 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 71 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: A 201 ASP cc_start: 0.8093 (p0) cc_final: 0.7820 (p0) REVERT: A 207 ASP cc_start: 0.7778 (t0) cc_final: 0.7408 (t0) REVERT: A 251 GLU cc_start: 0.7674 (tt0) cc_final: 0.7425 (tt0) REVERT: A 284 ARG cc_start: 0.3351 (ttt180) cc_final: 0.0915 (tmt170) REVERT: A 397 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7069 (mm-30) REVERT: A 408 THR cc_start: 0.8549 (m) cc_final: 0.8236 (p) REVERT: A 411 ASP cc_start: 0.8036 (t0) cc_final: 0.7686 (t0) REVERT: A 463 GLU cc_start: 0.5158 (tp30) cc_final: 0.4813 (tp30) REVERT: A 483 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8037 (ttt-90) REVERT: A 512 ASP cc_start: 0.7991 (t0) cc_final: 0.7738 (t0) REVERT: A 525 MET cc_start: 0.8170 (mmm) cc_final: 0.7857 (mtm) REVERT: A 549 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8539 (ptp-110) REVERT: A 585 ASP cc_start: 0.7616 (OUTLIER) cc_final: 0.7200 (t0) outliers start: 13 outliers final: 6 residues processed: 79 average time/residue: 1.1681 time to fit residues: 96.0630 Evaluate side-chains 81 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 483 ARG Chi-restraints excluded: chain A residue 549 ARG Chi-restraints excluded: chain A residue 585 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4620 Z= 0.204 Angle : 0.568 6.942 6271 Z= 0.300 Chirality : 0.044 0.174 714 Planarity : 0.003 0.031 797 Dihedral : 4.679 30.868 890 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.52 % Allowed : 17.86 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.16 (0.36), residues: 533 helix: 0.91 (0.66), residues: 66 sheet: 0.58 (0.44), residues: 148 loop : -0.24 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 129 HIS 0.007 0.001 HIS A 155 PHE 0.012 0.001 PHE A 486 TYR 0.027 0.001 TYR A 97 ARG 0.002 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 192 ASP cc_start: 0.7921 (m-30) cc_final: 0.7672 (m-30) REVERT: A 201 ASP cc_start: 0.8073 (p0) cc_final: 0.7793 (p0) REVERT: A 207 ASP cc_start: 0.7770 (t0) cc_final: 0.7405 (t0) REVERT: A 251 GLU cc_start: 0.7675 (tt0) cc_final: 0.7416 (tt0) REVERT: A 284 ARG cc_start: 0.3405 (ttt180) cc_final: 0.1154 (ppt170) REVERT: A 397 GLU cc_start: 0.7306 (mm-30) cc_final: 0.6960 (mm-30) REVERT: A 398 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7233 (mm-30) REVERT: A 408 THR cc_start: 0.8545 (m) cc_final: 0.8234 (p) REVERT: A 411 ASP cc_start: 0.8037 (t0) cc_final: 0.7681 (t0) REVERT: A 463 GLU cc_start: 0.5047 (tp30) cc_final: 0.4706 (tp30) REVERT: A 483 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8034 (ttt-90) REVERT: A 512 ASP cc_start: 0.7979 (t0) cc_final: 0.7715 (t0) REVERT: A 525 MET cc_start: 0.8183 (mmm) cc_final: 0.7857 (mtm) REVERT: A 549 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8535 (ptp-110) REVERT: A 585 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7192 (t0) outliers start: 12 outliers final: 5 residues processed: 81 average time/residue: 1.1739 time to fit residues: 98.9264 Evaluate side-chains 80 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 483 ARG Chi-restraints excluded: chain A residue 549 ARG Chi-restraints excluded: chain A residue 585 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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: 0.8349 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 4620 Z= 0.254 Angle : 0.608 12.357 6271 Z= 0.319 Chirality : 0.045 0.175 714 Planarity : 0.003 0.031 797 Dihedral : 4.755 31.796 890 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.10 % Allowed : 18.07 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 (0.36), residues: 533 helix: 0.91 (0.67), residues: 66 sheet: 0.53 (0.44), residues: 148 loop : -0.27 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 129 HIS 0.007 0.001 HIS A 155 PHE 0.012 0.001 PHE A 486 TYR 0.012 0.001 TYR A 97 ARG 0.004 0.000 ARG A 561 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 ASP cc_start: 0.7883 (m-30) cc_final: 0.7638 (m-30) REVERT: A 201 ASP cc_start: 0.8081 (p0) cc_final: 0.7794 (p0) REVERT: A 207 ASP cc_start: 0.7772 (t0) cc_final: 0.7399 (t0) REVERT: A 251 GLU cc_start: 0.7678 (tt0) cc_final: 0.7422 (tt0) REVERT: A 284 ARG cc_start: 0.3511 (ttt180) cc_final: 0.1158 (ppt170) REVERT: A 299 GLU cc_start: 0.7336 (mt-10) cc_final: 0.7023 (mp0) REVERT: A 408 THR cc_start: 0.8550 (m) cc_final: 0.8238 (p) REVERT: A 411 ASP cc_start: 0.8044 (t0) cc_final: 0.7670 (t0) REVERT: A 463 GLU cc_start: 0.5132 (tp30) cc_final: 0.4767 (tp30) REVERT: A 483 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8040 (ttt-90) REVERT: A 512 ASP cc_start: 0.7989 (t0) cc_final: 0.7731 (t0) REVERT: A 525 MET cc_start: 0.8185 (mmm) cc_final: 0.7880 (mtm) REVERT: A 549 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8539 (ptp-110) REVERT: A 585 ASP cc_start: 0.7618 (OUTLIER) cc_final: 0.7207 (t0) outliers start: 10 outliers final: 5 residues processed: 87 average time/residue: 1.0983 time to fit residues: 99.6412 Evaluate side-chains 75 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 483 ARG Chi-restraints excluded: chain A residue 549 ARG Chi-restraints excluded: chain A residue 585 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.089551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.080153 restraints weight = 7734.765| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.21 r_work: 0.3062 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 4620 Z= 0.224 Angle : 0.633 14.829 6271 Z= 0.326 Chirality : 0.044 0.179 714 Planarity : 0.003 0.029 797 Dihedral : 4.868 42.211 890 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.10 % Allowed : 19.33 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 (0.36), residues: 533 helix: 0.96 (0.66), residues: 66 sheet: 0.49 (0.45), residues: 148 loop : -0.26 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 129 HIS 0.007 0.001 HIS A 155 PHE 0.012 0.001 PHE A 486 TYR 0.032 0.001 TYR A 97 ARG 0.002 0.000 ARG A 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2269.72 seconds wall clock time: 40 minutes 57.10 seconds (2457.10 seconds total)