Starting phenix.real_space_refine on Tue Sep 24 02:56:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li7_23362/09_2024/7li7_23362.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li7_23362/09_2024/7li7_23362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li7_23362/09_2024/7li7_23362.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li7_23362/09_2024/7li7_23362.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li7_23362/09_2024/7li7_23362.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li7_23362/09_2024/7li7_23362.cif" } resolution = 4.1 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= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 4101 2.51 5 N 960 2.21 5 O 1082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6177 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4292 Classifications: {'peptide': 537} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 514} Chain: "B" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "C" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 830 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} 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: "A" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 114 Unusual residues: {'CLR': 1, 'D10': 1, 'D12': 3, 'HP6': 5, 'LNK': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Time building chain proxies: 5.57, per 1000 atoms: 0.90 Number of scatterers: 6177 At special positions: 0 Unit cell: (71.928, 73.224, 121.176, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1082 8.00 N 960 7.00 C 4101 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 115 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 112 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG D 1 " - " ASN A 208 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 1.1 seconds 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1396 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 9 sheets defined 54.0% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 84 through 97 Processing helix chain 'A' and resid 98 through 113 Proline residue: A 106 - end of helix Processing helix chain 'A' and resid 114 through 118 removed outlier: 3.758A pdb=" N LEU A 118 " --> pdb=" O GLY A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 144 Proline residue: A 131 - end of helix removed outlier: 3.841A pdb=" N GLU A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 154 removed outlier: 3.849A pdb=" N TRP A 151 " --> pdb=" O ILE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 158 Processing helix chain 'A' and resid 159 through 190 removed outlier: 4.289A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N THR A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 235 removed outlier: 3.615A pdb=" N HIS A 235 " --> pdb=" O PHE A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 252 through 271 Processing helix chain 'A' and resid 273 through 282 removed outlier: 3.730A pdb=" N TRP A 282 " --> pdb=" O GLY A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 300 removed outlier: 4.143A pdb=" N TYR A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 313 Processing helix chain 'A' and resid 325 through 338 Processing helix chain 'A' and resid 342 through 349 Processing helix chain 'A' and resid 356 through 391 Processing helix chain 'A' and resid 403 through 417 removed outlier: 4.240A pdb=" N PHE A 407 " --> pdb=" O PRO A 403 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA A 411 " --> pdb=" O PHE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 448 removed outlier: 3.836A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 454 removed outlier: 3.608A pdb=" N GLU A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 461 removed outlier: 4.125A pdb=" N LYS A 460 " --> pdb=" O HIS A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 484 removed outlier: 3.708A pdb=" N VAL A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 483 " --> pdb=" O VAL A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 496 Processing helix chain 'A' and resid 498 through 514 Processing helix chain 'A' and resid 517 through 530 removed outlier: 4.456A pdb=" N ASP A 524 " --> pdb=" O GLN A 520 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL A 525 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU A 527 " --> pdb=" O ARG A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 541 Processing helix chain 'A' and resid 543 through 559 removed outlier: 3.768A pdb=" N ILE A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 585 Processing helix chain 'A' and resid 587 through 600 Processing helix chain 'A' and resid 603 through 612 Processing sheet with id=AA1, first strand: chain 'B' and resid 24 through 25 Processing sheet with id=AA2, first strand: chain 'B' and resid 38 through 39 removed outlier: 3.711A pdb=" N ILE B 39 " --> pdb=" O MET B 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 77 through 79 removed outlier: 3.559A pdb=" N ARG B 69 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TRP B 55 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ARG B 69 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N MET B 53 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 77 through 79 removed outlier: 3.559A pdb=" N ARG B 69 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TRP B 55 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ARG B 69 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N MET B 53 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 25 through 27 removed outlier: 3.515A pdb=" N ALA C 39 " --> pdb=" O ILE C 99 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE C 95 " --> pdb=" O CYS C 43 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR C 94 " --> pdb=" O SER C 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 30 through 32 removed outlier: 6.241A pdb=" N LEU C 31 " --> pdb=" O GLU C 129 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR C 126 " --> pdb=" O TYR C 110 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR C 110 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE C 111 " --> pdb=" O PHE C 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 30 through 32 removed outlier: 6.241A pdb=" N LEU C 31 " --> pdb=" O GLU C 129 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR C 126 " --> pdb=" O TYR C 110 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR C 110 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR C 121 " --> pdb=" O GLN C 114 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 50 through 51 removed outlier: 3.587A pdb=" N ASN C 51 " --> pdb=" O ILE C 54 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 72 through 73 319 hydrogen bonds defined for protein. 900 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: 1.92 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1814 1.34 - 1.46: 1597 1.46 - 1.58: 2889 1.58 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 6349 Sorted by residual: bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" N SER C 48 " pdb=" CA SER C 48 " ideal model delta sigma weight residual 1.458 1.482 -0.024 1.90e-02 2.77e+03 1.64e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.51e+00 bond pdb=" C GLU C 47 " pdb=" N SER C 48 " ideal model delta sigma weight residual 1.329 1.345 -0.016 1.40e-02 5.10e+03 1.35e+00 bond pdb=" C5 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.21e+00 ... (remaining 6344 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 8434 1.88 - 3.75: 125 3.75 - 5.63: 49 5.63 - 7.50: 3 7.50 - 9.38: 1 Bond angle restraints: 8612 Sorted by residual: angle pdb=" C GLU C 47 " pdb=" N SER C 48 " pdb=" CA SER C 48 " ideal model delta sigma weight residual 121.70 131.08 -9.38 1.80e+00 3.09e-01 2.71e+01 angle pdb=" N TRP A 197 " pdb=" CA TRP A 197 " pdb=" C TRP A 197 " ideal model delta sigma weight residual 114.56 111.00 3.56 1.27e+00 6.20e-01 7.84e+00 angle pdb=" C13 CLR A 710 " pdb=" C17 CLR A 710 " pdb=" C20 CLR A 710 " ideal model delta sigma weight residual 119.60 112.55 7.05 3.00e+00 1.11e-01 5.52e+00 angle pdb=" C20 CLR A 710 " pdb=" C22 CLR A 710 " pdb=" C23 CLR A 710 " ideal model delta sigma weight residual 115.57 108.76 6.81 3.00e+00 1.11e-01 5.16e+00 angle pdb=" CA GLU C 47 " pdb=" C GLU C 47 " pdb=" N SER C 48 " ideal model delta sigma weight residual 115.49 118.10 -2.61 1.24e+00 6.50e-01 4.42e+00 ... (remaining 8607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 3379 17.81 - 35.61: 284 35.61 - 53.42: 40 53.42 - 71.23: 5 71.23 - 89.03: 2 Dihedral angle restraints: 3710 sinusoidal: 1510 harmonic: 2200 Sorted by residual: dihedral pdb=" CB GLU A 453 " pdb=" CG GLU A 453 " pdb=" CD GLU A 453 " pdb=" OE1 GLU A 453 " ideal model delta sinusoidal sigma weight residual 0.00 89.03 -89.03 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU A 136 " pdb=" CG GLU A 136 " pdb=" CD GLU A 136 " pdb=" OE1 GLU A 136 " ideal model delta sinusoidal sigma weight residual 0.00 -84.87 84.87 1 3.00e+01 1.11e-03 9.71e+00 dihedral pdb=" CA ARG A 596 " pdb=" CB ARG A 596 " pdb=" CG ARG A 596 " pdb=" CD ARG A 596 " ideal model delta sinusoidal sigma weight residual 180.00 122.06 57.94 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 3707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.234: 945 0.234 - 0.469: 2 0.469 - 0.703: 0 0.703 - 0.937: 0 0.937 - 1.171: 1 Chirality restraints: 948 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.23 -1.17 2.00e-02 2.50e+03 3.43e+03 chirality pdb=" C14 CLR A 710 " pdb=" C13 CLR A 710 " pdb=" C15 CLR A 710 " pdb=" C8 CLR A 710 " both_signs ideal model delta sigma weight residual False -2.32 -2.67 0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" C9 CLR A 710 " pdb=" C10 CLR A 710 " pdb=" C11 CLR A 710 " pdb=" C8 CLR A 710 " both_signs ideal model delta sigma weight residual False -2.45 -2.70 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 945 not shown) Planarity restraints: 1048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 402 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO A 403 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 403 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 403 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 100 " -0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO C 101 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO C 101 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 101 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 589 " -0.016 5.00e-02 4.00e+02 2.41e-02 9.26e-01 pdb=" N PRO A 590 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 590 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 590 " -0.014 5.00e-02 4.00e+02 ... (remaining 1045 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1874 2.82 - 3.34: 5815 3.34 - 3.86: 10355 3.86 - 4.38: 11298 4.38 - 4.90: 19568 Nonbonded interactions: 48910 Sorted by model distance: nonbonded pdb=" OH TYR A 110 " pdb=" O VAL A 397 " model vdw 2.297 3.040 nonbonded pdb=" O ASN A 112 " pdb=" NZ LYS A 319 " model vdw 2.304 3.120 nonbonded pdb=" O THR A 600 " pdb=" NE ARG A 607 " model vdw 2.304 3.120 nonbonded pdb=" OD1 ASN A 101 " pdb=" NE2 GLN A 332 " model vdw 2.311 3.120 nonbonded pdb=" O SER A 190 " pdb=" OG SER A 190 " model vdw 2.313 3.040 ... (remaining 48905 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.520 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6461 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 : 0.002 0.031 6349 Z= 0.142 Angle : 0.611 9.376 8612 Z= 0.297 Chirality : 0.056 1.171 948 Planarity : 0.003 0.034 1047 Dihedral : 12.289 89.034 2305 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.27), residues: 759 helix: -0.80 (0.24), residues: 370 sheet: -1.58 (0.54), residues: 81 loop : -3.08 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 204 HIS 0.001 0.000 HIS A 143 PHE 0.016 0.001 PHE A 474 TYR 0.012 0.001 TYR A 176 ARG 0.006 0.000 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.4133 (mmmt) cc_final: 0.3539 (mmtp) REVERT: A 260 MET cc_start: 0.6096 (mmm) cc_final: 0.4406 (tmm) REVERT: A 267 TYR cc_start: 0.7045 (t80) cc_final: 0.6839 (t80) REVERT: A 456 HIS cc_start: 0.7952 (p-80) cc_final: 0.7737 (p90) REVERT: A 463 GLU cc_start: 0.7079 (tm-30) cc_final: 0.6779 (mm-30) REVERT: A 478 LEU cc_start: 0.6966 (tt) cc_final: 0.6669 (tp) REVERT: A 514 TRP cc_start: 0.6695 (m100) cc_final: 0.6023 (m-10) REVERT: B 29 GLU cc_start: 0.8859 (mp0) cc_final: 0.8552 (mp0) REVERT: B 88 THR cc_start: 0.9257 (m) cc_final: 0.8963 (p) REVERT: B 125 PHE cc_start: 0.8290 (m-80) cc_final: 0.7888 (m-10) REVERT: C 33 VAL cc_start: 0.8265 (m) cc_final: 0.8057 (p) REVERT: C 66 GLN cc_start: 0.7811 (mp10) cc_final: 0.7283 (mp10) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.2320 time to fit residues: 45.7915 Evaluate side-chains 117 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 0.0040 chunk 30 optimal weight: 0.5980 chunk 58 optimal weight: 0.4980 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 43 optimal weight: 0.2980 chunk 68 optimal weight: 5.9990 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 GLN ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN B 58 GLN B 132 GLN ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 6349 Z= 0.170 Angle : 0.535 9.376 8612 Z= 0.277 Chirality : 0.040 0.178 948 Planarity : 0.005 0.091 1047 Dihedral : 5.769 59.224 995 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.31 % Allowed : 4.36 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -1.88 (0.29), residues: 759 helix: -0.00 (0.26), residues: 370 sheet: -1.61 (0.53), residues: 90 loop : -2.73 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 317 HIS 0.002 0.001 HIS A 143 PHE 0.016 0.001 PHE A 474 TYR 0.014 0.001 TYR B 99 ARG 0.004 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 143 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 SER cc_start: 0.8942 (t) cc_final: 0.8693 (t) REVERT: A 201 LYS cc_start: 0.4361 (mmmt) cc_final: 0.3937 (mmmt) REVERT: A 267 TYR cc_start: 0.7296 (t80) cc_final: 0.7059 (t80) REVERT: A 514 TRP cc_start: 0.6669 (m100) cc_final: 0.6043 (m-10) REVERT: B 32 LYS cc_start: 0.6081 (mmpt) cc_final: 0.5722 (mmmt) REVERT: B 57 LYS cc_start: 0.8838 (tttm) cc_final: 0.8219 (ttmm) REVERT: B 88 THR cc_start: 0.9431 (m) cc_final: 0.9164 (p) REVERT: C 66 GLN cc_start: 0.8126 (mp10) cc_final: 0.7763 (mp10) outliers start: 2 outliers final: 0 residues processed: 144 average time/residue: 0.1868 time to fit residues: 35.3134 Evaluate side-chains 117 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 67 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 GLN C 61 GLN C 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6349 Z= 0.277 Angle : 0.610 9.605 8612 Z= 0.321 Chirality : 0.042 0.152 948 Planarity : 0.005 0.060 1047 Dihedral : 6.050 59.479 995 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.47 % Allowed : 5.92 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -1.65 (0.29), residues: 759 helix: 0.14 (0.26), residues: 369 sheet: -1.62 (0.50), residues: 100 loop : -2.50 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 541 HIS 0.005 0.001 HIS A 143 PHE 0.020 0.002 PHE A 474 TYR 0.017 0.002 TYR A 186 ARG 0.006 0.001 ARG A 596 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 135 time to evaluate : 0.660 Fit side-chains REVERT: A 80 GLU cc_start: 0.7648 (tm-30) cc_final: 0.6931 (tm-30) REVERT: A 197 TRP cc_start: 0.7525 (m-90) cc_final: 0.7243 (m-10) REVERT: A 201 LYS cc_start: 0.4697 (mmmt) cc_final: 0.4179 (mmtt) REVERT: A 267 TYR cc_start: 0.7636 (t80) cc_final: 0.7302 (t80) REVERT: A 456 HIS cc_start: 0.7853 (p90) cc_final: 0.7612 (p90) REVERT: A 514 TRP cc_start: 0.6741 (m100) cc_final: 0.6134 (m-10) REVERT: B 32 LYS cc_start: 0.6248 (mmpt) cc_final: 0.5948 (mmmt) REVERT: B 59 ARG cc_start: 0.8359 (mtp85) cc_final: 0.8124 (mtm-85) REVERT: B 88 THR cc_start: 0.9493 (m) cc_final: 0.9180 (p) REVERT: C 62 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8400 (tt0) REVERT: C 86 PHE cc_start: 0.7912 (m-80) cc_final: 0.7480 (m-10) outliers start: 3 outliers final: 0 residues processed: 137 average time/residue: 0.1789 time to fit residues: 32.6268 Evaluate side-chains 112 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 GLN A 217 ASN A 235 HIS B 101 GLN B 132 GLN C 62 GLN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 6349 Z= 0.270 Angle : 0.596 9.837 8612 Z= 0.315 Chirality : 0.042 0.161 948 Planarity : 0.004 0.070 1047 Dihedral : 6.339 59.630 995 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.31 % Allowed : 4.67 % Favored : 95.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -1.45 (0.30), residues: 759 helix: 0.33 (0.27), residues: 370 sheet: -1.37 (0.52), residues: 95 loop : -2.51 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 541 HIS 0.004 0.001 HIS A 143 PHE 0.022 0.002 PHE A 474 TYR 0.018 0.002 TYR A 186 ARG 0.003 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 135 time to evaluate : 0.626 Fit side-chains REVERT: A 186 TYR cc_start: 0.8176 (m-10) cc_final: 0.7971 (m-10) REVERT: A 201 LYS cc_start: 0.4809 (mmmt) cc_final: 0.4071 (mmtt) REVERT: A 456 HIS cc_start: 0.7826 (p90) cc_final: 0.7541 (p90) REVERT: A 514 TRP cc_start: 0.6707 (m100) cc_final: 0.6084 (m-10) REVERT: A 536 PHE cc_start: 0.8840 (t80) cc_final: 0.8215 (t80) REVERT: A 576 ILE cc_start: 0.7835 (tp) cc_final: 0.7591 (tp) REVERT: B 32 LYS cc_start: 0.6143 (mmpt) cc_final: 0.5899 (mmmt) REVERT: B 59 ARG cc_start: 0.8326 (mtp85) cc_final: 0.8103 (mtm-85) REVERT: B 65 GLU cc_start: 0.7499 (mt-10) cc_final: 0.6324 (mt-10) REVERT: B 88 THR cc_start: 0.9513 (m) cc_final: 0.9212 (p) REVERT: B 109 ASP cc_start: 0.8335 (p0) cc_final: 0.7935 (p0) REVERT: C 33 VAL cc_start: 0.8789 (m) cc_final: 0.8582 (p) REVERT: C 66 GLN cc_start: 0.8422 (mp10) cc_final: 0.8051 (mp10) REVERT: C 86 PHE cc_start: 0.7989 (m-80) cc_final: 0.7757 (m-80) outliers start: 2 outliers final: 1 residues processed: 137 average time/residue: 0.1835 time to fit residues: 33.2099 Evaluate side-chains 110 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 65 optimal weight: 0.0870 chunk 18 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 GLN ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 GLN C 62 GLN C 66 GLN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6349 Z= 0.213 Angle : 0.577 9.886 8612 Z= 0.302 Chirality : 0.042 0.222 948 Planarity : 0.004 0.065 1047 Dihedral : 6.306 59.879 995 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.16 % Allowed : 2.65 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -1.35 (0.30), residues: 759 helix: 0.37 (0.27), residues: 367 sheet: -1.30 (0.51), residues: 100 loop : -2.40 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 541 HIS 0.003 0.001 HIS A 143 PHE 0.020 0.001 PHE A 474 TYR 0.016 0.002 TYR A 107 ARG 0.007 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 138 time to evaluate : 0.743 Fit side-chains REVERT: A 141 GLN cc_start: 0.7248 (OUTLIER) cc_final: 0.7047 (pp30) REVERT: A 201 LYS cc_start: 0.4783 (mmmt) cc_final: 0.3889 (mmmt) REVERT: A 456 HIS cc_start: 0.7824 (p90) cc_final: 0.7523 (p90) REVERT: A 514 TRP cc_start: 0.6743 (m100) cc_final: 0.6139 (m-10) REVERT: A 536 PHE cc_start: 0.8713 (t80) cc_final: 0.7837 (t80) REVERT: A 576 ILE cc_start: 0.7805 (tp) cc_final: 0.7541 (tp) REVERT: B 32 LYS cc_start: 0.6058 (mmpt) cc_final: 0.5810 (mmmt) REVERT: B 65 GLU cc_start: 0.7492 (mt-10) cc_final: 0.6373 (mt-10) REVERT: B 88 THR cc_start: 0.9508 (m) cc_final: 0.9208 (p) REVERT: B 100 MET cc_start: 0.8146 (ttt) cc_final: 0.7919 (ttp) REVERT: C 33 VAL cc_start: 0.8727 (m) cc_final: 0.8522 (p) REVERT: C 66 GLN cc_start: 0.8350 (mp10) cc_final: 0.7710 (mp10) REVERT: C 86 PHE cc_start: 0.7945 (m-80) cc_final: 0.7690 (m-80) outliers start: 1 outliers final: 0 residues processed: 139 average time/residue: 0.1880 time to fit residues: 34.6487 Evaluate side-chains 113 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 0.0170 chunk 24 optimal weight: 0.0670 chunk 38 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 ASN C 62 GLN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6349 Z= 0.199 Angle : 0.594 9.746 8612 Z= 0.307 Chirality : 0.042 0.205 948 Planarity : 0.004 0.069 1047 Dihedral : 6.358 59.965 995 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -1.22 (0.30), residues: 759 helix: 0.46 (0.27), residues: 367 sheet: -1.08 (0.52), residues: 100 loop : -2.37 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 317 HIS 0.003 0.001 HIS A 143 PHE 0.020 0.001 PHE A 474 TYR 0.018 0.001 TYR A 107 ARG 0.006 0.001 ARG C 85 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.806 Fit side-chains REVERT: A 186 TYR cc_start: 0.8435 (m-10) cc_final: 0.8159 (m-80) REVERT: A 201 LYS cc_start: 0.4836 (mmmt) cc_final: 0.3909 (mmmt) REVERT: A 456 HIS cc_start: 0.7794 (p90) cc_final: 0.7459 (p90) REVERT: A 514 TRP cc_start: 0.6742 (m100) cc_final: 0.6172 (m-10) REVERT: A 536 PHE cc_start: 0.8731 (t80) cc_final: 0.7810 (t80) REVERT: B 32 LYS cc_start: 0.6046 (mmpt) cc_final: 0.5806 (mmmt) REVERT: B 59 ARG cc_start: 0.7738 (mtm-85) cc_final: 0.7149 (mtm-85) REVERT: B 65 GLU cc_start: 0.7383 (mt-10) cc_final: 0.6607 (mt-10) REVERT: B 88 THR cc_start: 0.9479 (m) cc_final: 0.9174 (p) REVERT: B 99 TYR cc_start: 0.8381 (m-10) cc_final: 0.7957 (m-10) REVERT: C 33 VAL cc_start: 0.8702 (m) cc_final: 0.8464 (p) REVERT: C 66 GLN cc_start: 0.8338 (mp10) cc_final: 0.7828 (mp10) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1876 time to fit residues: 32.8173 Evaluate side-chains 114 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 GLN C 62 GLN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6349 Z= 0.266 Angle : 0.621 9.855 8612 Z= 0.327 Chirality : 0.043 0.183 948 Planarity : 0.005 0.067 1047 Dihedral : 6.564 59.768 995 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.16 % Allowed : 1.56 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -1.17 (0.31), residues: 759 helix: 0.44 (0.27), residues: 368 sheet: -0.94 (0.54), residues: 100 loop : -2.33 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 317 HIS 0.005 0.001 HIS A 143 PHE 0.020 0.002 PHE A 474 TYR 0.016 0.002 TYR A 107 ARG 0.006 0.000 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: A 186 TYR cc_start: 0.8463 (m-10) cc_final: 0.8195 (m-80) REVERT: A 201 LYS cc_start: 0.5039 (mmmt) cc_final: 0.4064 (mmmt) REVERT: A 414 ILE cc_start: 0.7206 (mm) cc_final: 0.6800 (mm) REVERT: A 456 HIS cc_start: 0.7791 (p90) cc_final: 0.7417 (p90) REVERT: A 514 TRP cc_start: 0.6909 (m100) cc_final: 0.6306 (m-10) REVERT: A 536 PHE cc_start: 0.8798 (t80) cc_final: 0.7904 (t80) REVERT: A 537 TRP cc_start: 0.7231 (m-90) cc_final: 0.6938 (m-90) REVERT: A 576 ILE cc_start: 0.7887 (tp) cc_final: 0.7599 (tp) REVERT: B 32 LYS cc_start: 0.6053 (mmpt) cc_final: 0.5821 (mmmt) REVERT: B 59 ARG cc_start: 0.7749 (mtm-85) cc_final: 0.7243 (mtm-85) REVERT: B 65 GLU cc_start: 0.7452 (mt-10) cc_final: 0.6654 (mt-10) REVERT: B 88 THR cc_start: 0.9499 (m) cc_final: 0.9207 (p) REVERT: C 33 VAL cc_start: 0.8755 (m) cc_final: 0.8516 (p) outliers start: 1 outliers final: 0 residues processed: 136 average time/residue: 0.1627 time to fit residues: 30.4135 Evaluate side-chains 114 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 0.2980 chunk 45 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6349 Z= 0.211 Angle : 0.592 9.868 8612 Z= 0.312 Chirality : 0.042 0.194 948 Planarity : 0.005 0.072 1047 Dihedral : 6.581 59.907 995 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.16 % Allowed : 0.93 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -1.07 (0.31), residues: 759 helix: 0.47 (0.27), residues: 369 sheet: -0.81 (0.54), residues: 100 loop : -2.23 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 317 HIS 0.003 0.001 HIS A 143 PHE 0.022 0.001 PHE A 474 TYR 0.020 0.001 TYR A 107 ARG 0.004 0.000 ARG A 596 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 0.645 Fit side-chains REVERT: A 186 TYR cc_start: 0.8448 (m-10) cc_final: 0.8166 (m-80) REVERT: A 201 LYS cc_start: 0.4992 (mmmt) cc_final: 0.4039 (mmmt) REVERT: A 514 TRP cc_start: 0.6917 (m100) cc_final: 0.6296 (m-10) REVERT: A 536 PHE cc_start: 0.8790 (t80) cc_final: 0.7924 (t80) REVERT: A 537 TRP cc_start: 0.7268 (m-90) cc_final: 0.6941 (m-90) REVERT: A 576 ILE cc_start: 0.7859 (tp) cc_final: 0.7563 (tp) REVERT: B 32 LYS cc_start: 0.6107 (mmpt) cc_final: 0.5894 (mmmt) REVERT: B 59 ARG cc_start: 0.7790 (mtm-85) cc_final: 0.7368 (mtm-85) REVERT: B 65 GLU cc_start: 0.7422 (mt-10) cc_final: 0.6619 (mt-10) REVERT: B 86 LYS cc_start: 0.8185 (ptmt) cc_final: 0.7961 (tttt) REVERT: B 88 THR cc_start: 0.9503 (m) cc_final: 0.9209 (p) REVERT: B 99 TYR cc_start: 0.8611 (m-10) cc_final: 0.7966 (m-80) REVERT: C 33 VAL cc_start: 0.8781 (m) cc_final: 0.8568 (p) REVERT: C 37 GLN cc_start: 0.8552 (pm20) cc_final: 0.8287 (pm20) REVERT: C 66 GLN cc_start: 0.8432 (mp10) cc_final: 0.7891 (mp10) outliers start: 1 outliers final: 1 residues processed: 129 average time/residue: 0.1564 time to fit residues: 27.7709 Evaluate side-chains 108 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 0.0470 chunk 40 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 63 optimal weight: 0.3980 chunk 67 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN C 98 ASN ** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6349 Z= 0.222 Angle : 0.607 11.896 8612 Z= 0.319 Chirality : 0.043 0.182 948 Planarity : 0.005 0.070 1047 Dihedral : 6.604 59.996 995 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -0.99 (0.31), residues: 759 helix: 0.51 (0.27), residues: 369 sheet: -0.83 (0.54), residues: 100 loop : -2.13 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 317 HIS 0.005 0.001 HIS C 100 PHE 0.021 0.001 PHE A 474 TYR 0.017 0.001 TYR A 107 ARG 0.003 0.000 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.669 Fit side-chains REVERT: A 186 TYR cc_start: 0.8501 (m-10) cc_final: 0.8209 (m-80) REVERT: A 201 LYS cc_start: 0.5001 (mmmt) cc_final: 0.4043 (mmmt) REVERT: A 456 HIS cc_start: 0.7774 (p90) cc_final: 0.7463 (p90) REVERT: A 514 TRP cc_start: 0.6942 (m100) cc_final: 0.6294 (m-10) REVERT: A 536 PHE cc_start: 0.8826 (t80) cc_final: 0.7989 (t80) REVERT: A 576 ILE cc_start: 0.7892 (tp) cc_final: 0.7594 (tp) REVERT: B 32 LYS cc_start: 0.6111 (mmpt) cc_final: 0.5903 (mmmt) REVERT: B 59 ARG cc_start: 0.7721 (mtm-85) cc_final: 0.7334 (mtm-85) REVERT: B 65 GLU cc_start: 0.7406 (mt-10) cc_final: 0.6628 (mt-10) REVERT: B 88 THR cc_start: 0.9515 (m) cc_final: 0.9229 (p) REVERT: B 99 TYR cc_start: 0.8712 (m-10) cc_final: 0.8041 (m-80) REVERT: C 33 VAL cc_start: 0.8836 (m) cc_final: 0.8575 (p) REVERT: C 103 GLU cc_start: 0.6989 (pp20) cc_final: 0.6732 (pp20) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1607 time to fit residues: 27.1539 Evaluate side-chains 109 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 0.6980 chunk 49 optimal weight: 0.2980 chunk 74 optimal weight: 0.9980 chunk 68 optimal weight: 0.0020 chunk 59 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 45 optimal weight: 0.0270 chunk 36 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 63 optimal weight: 0.0980 chunk 18 optimal weight: 0.5980 overall best weight: 0.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN ** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6349 Z= 0.164 Angle : 0.591 11.387 8612 Z= 0.312 Chirality : 0.042 0.192 948 Planarity : 0.005 0.075 1047 Dihedral : 6.528 59.655 995 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.16 % Allowed : 0.16 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -0.88 (0.31), residues: 759 helix: 0.55 (0.27), residues: 371 sheet: -0.68 (0.55), residues: 98 loop : -2.03 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 317 HIS 0.002 0.001 HIS A 143 PHE 0.023 0.001 PHE A 127 TYR 0.019 0.001 TYR A 107 ARG 0.003 0.000 ARG A 607 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 0.663 Fit side-chains REVERT: A 186 TYR cc_start: 0.8365 (m-10) cc_final: 0.8165 (m-80) REVERT: A 201 LYS cc_start: 0.4832 (mmmt) cc_final: 0.3907 (mmmt) REVERT: A 456 HIS cc_start: 0.7766 (p90) cc_final: 0.7460 (p90) REVERT: A 514 TRP cc_start: 0.6936 (m100) cc_final: 0.6284 (m-10) REVERT: A 536 PHE cc_start: 0.8812 (t80) cc_final: 0.7887 (t80) REVERT: A 537 TRP cc_start: 0.7185 (m-90) cc_final: 0.6872 (m-90) REVERT: B 65 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6788 (mt-10) REVERT: B 88 THR cc_start: 0.9516 (m) cc_final: 0.9226 (p) REVERT: B 99 TYR cc_start: 0.8721 (m-10) cc_final: 0.8079 (m-80) REVERT: C 33 VAL cc_start: 0.8814 (m) cc_final: 0.8564 (p) REVERT: C 66 GLN cc_start: 0.8426 (mp10) cc_final: 0.8146 (mp10) REVERT: C 103 GLU cc_start: 0.6928 (pp20) cc_final: 0.6678 (pp20) outliers start: 1 outliers final: 1 residues processed: 122 average time/residue: 0.1619 time to fit residues: 26.9746 Evaluate side-chains 107 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 0.0870 chunk 61 optimal weight: 6.9990 chunk 7 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 chunk 52 optimal weight: 8.9990 chunk 3 optimal weight: 0.5980 chunk 43 optimal weight: 0.0060 overall best weight: 0.3974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN ** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.193801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.186746 restraints weight = 7452.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.173291 restraints weight = 14215.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.169214 restraints weight = 13869.082| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6349 Z= 0.185 Angle : 0.607 11.208 8612 Z= 0.317 Chirality : 0.042 0.178 948 Planarity : 0.005 0.071 1047 Dihedral : 6.499 59.616 995 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.31), residues: 759 helix: 0.59 (0.27), residues: 367 sheet: -0.81 (0.53), residues: 103 loop : -2.10 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 317 HIS 0.003 0.001 HIS A 143 PHE 0.020 0.001 PHE A 556 TYR 0.037 0.001 TYR A 410 ARG 0.006 0.000 ARG B 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1812.29 seconds wall clock time: 33 minutes 31.05 seconds (2011.05 seconds total)