Starting phenix.real_space_refine on Sun Mar 10 19:02:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y0o_33551/03_2024/7y0o_33551.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y0o_33551/03_2024/7y0o_33551.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y0o_33551/03_2024/7y0o_33551.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y0o_33551/03_2024/7y0o_33551.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y0o_33551/03_2024/7y0o_33551.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y0o_33551/03_2024/7y0o_33551.pdb" } resolution = 4.4 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= 0.042 sd= 1.426 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 19 5.16 5 C 2644 2.51 5 N 701 2.21 5 O 821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 389": "OD1" <-> "OD2" Residue "A PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 74": "OE1" <-> "OE2" Residue "H ASP 89": "OD1" <-> "OD2" Residue "L ASP 28": "OD1" <-> "OD2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "B TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 4185 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1513 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 11, 'TRANS': 182} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 22 Chain: "H" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 889 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 818 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 947 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Time building chain proxies: 2.76, per 1000 atoms: 0.66 Number of scatterers: 4185 At special positions: 0 Unit cell: (85.6, 87.74, 111.28, 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 19 16.00 O 821 8.00 N 701 7.00 C 2644 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 741.0 milliseconds 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: 980 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 11 sheets defined 7.4% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.521A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 5.878A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.824A pdb=" N ASN A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 65 removed outlier: 3.673A pdb=" N GLN H 65 " --> pdb=" O GLN H 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 358 removed outlier: 4.393A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR A 508 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'H' and resid 16 through 17 removed outlier: 3.942A pdb=" N ALA H 16 " --> pdb=" O SER H 85 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER H 85 " --> pdb=" O ALA H 16 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'H' and resid 22 through 23 removed outlier: 3.827A pdb=" N GLU H 82 " --> pdb=" O THR H 69 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 45 through 51 removed outlier: 4.998A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER H 35 " --> pdb=" O ALA H 96 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.617A pdb=" N ALA L 13 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR L 49 " --> pdb=" O SER L 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 62 through 67 removed outlier: 3.623A pdb=" N SER L 65 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR L 72 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 6 through 7 removed outlier: 3.904A pdb=" N CYS B 22 " --> pdb=" O VAL B 79 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B 79 " --> pdb=" O CYS B 22 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 11 through 12 Processing sheet with id=AB2, first strand: chain 'B' and resid 58 through 60 removed outlier: 3.666A pdb=" N ARG B 59 " --> pdb=" O ASP B 50 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ALA B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ALA B 40 " --> pdb=" O ALA B 44 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) 77 hydrogen bonds defined for protein. 171 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: 1.12 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1337 1.35 - 1.47: 1148 1.47 - 1.59: 1764 1.59 - 1.71: 0 1.71 - 1.83: 24 Bond restraints: 4273 Sorted by residual: bond pdb=" CB GLN L 38 " pdb=" CG GLN L 38 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.31e+00 bond pdb=" C SER A 477 " pdb=" N THR A 478 " ideal model delta sigma weight residual 1.331 1.311 0.021 1.63e-02 3.76e+03 1.61e+00 bond pdb=" CA VAL A 483 " pdb=" CB VAL A 483 " ideal model delta sigma weight residual 1.547 1.568 -0.021 1.68e-02 3.54e+03 1.56e+00 bond pdb=" CG GLN L 38 " pdb=" CD GLN L 38 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.47e+00 bond pdb=" C GLY H 26 " pdb=" N TYR H 27 " ideal model delta sigma weight residual 1.325 1.339 -0.014 1.14e-02 7.69e+03 1.47e+00 ... (remaining 4268 not shown) Histogram of bond angle deviations from ideal: 98.41 - 105.58: 89 105.58 - 112.74: 2037 112.74 - 119.90: 1509 119.90 - 127.06: 2122 127.06 - 134.22: 48 Bond angle restraints: 5805 Sorted by residual: angle pdb=" C TYR H 27 " pdb=" CA TYR H 27 " pdb=" CB TYR H 27 " ideal model delta sigma weight residual 115.79 109.40 6.39 1.19e+00 7.06e-01 2.88e+01 angle pdb=" CB GLN L 38 " pdb=" CG GLN L 38 " pdb=" CD GLN L 38 " ideal model delta sigma weight residual 112.60 118.45 -5.85 1.70e+00 3.46e-01 1.19e+01 angle pdb=" CA LEU B 119 " pdb=" CB LEU B 119 " pdb=" CG LEU B 119 " ideal model delta sigma weight residual 116.30 127.53 -11.23 3.50e+00 8.16e-02 1.03e+01 angle pdb=" C ALA L 50 " pdb=" N ALA L 51 " pdb=" CA ALA L 51 " ideal model delta sigma weight residual 121.54 127.42 -5.88 1.91e+00 2.74e-01 9.49e+00 angle pdb=" C ASN A 354 " pdb=" N ARG A 355 " pdb=" CA ARG A 355 " ideal model delta sigma weight residual 122.59 127.38 -4.79 1.57e+00 4.06e-01 9.30e+00 ... (remaining 5800 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 2189 16.92 - 33.83: 248 33.83 - 50.75: 55 50.75 - 67.66: 8 67.66 - 84.57: 8 Dihedral angle restraints: 2508 sinusoidal: 954 harmonic: 1554 Sorted by residual: dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 11.68 81.32 1 1.00e+01 1.00e-02 8.15e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 161.12 -68.12 1 1.00e+01 1.00e-02 6.02e+01 dihedral pdb=" CA ASN A 481 " pdb=" C ASN A 481 " pdb=" N GLY A 482 " pdb=" CA GLY A 482 " ideal model delta harmonic sigma weight residual -180.00 -151.38 -28.62 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 2505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 539 0.085 - 0.170: 72 0.170 - 0.254: 2 0.254 - 0.339: 2 0.339 - 0.424: 1 Chirality restraints: 616 Sorted by residual: chirality pdb=" CB ILE A 410 " pdb=" CA ILE A 410 " pdb=" CG1 ILE A 410 " pdb=" CG2 ILE A 410 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.49e+00 chirality pdb=" CB ILE H 52 " pdb=" CA ILE H 52 " pdb=" CG1 ILE H 52 " pdb=" CG2 ILE H 52 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CB VAL B 98 " pdb=" CA VAL B 98 " pdb=" CG1 VAL B 98 " pdb=" CG2 VAL B 98 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 613 not shown) Planarity restraints: 755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 36 " -0.018 2.00e-02 2.50e+03 1.98e-02 9.80e+00 pdb=" CG TRP B 36 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP B 36 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP B 36 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 36 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 36 " 0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP B 36 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 36 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 36 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B 36 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 425 " 0.044 5.00e-02 4.00e+02 6.74e-02 7.26e+00 pdb=" N PRO A 426 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 426 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 426 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 353 " 0.014 2.00e-02 2.50e+03 1.70e-02 7.20e+00 pdb=" CG TRP A 353 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP A 353 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP A 353 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 353 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 353 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 353 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 353 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 353 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP A 353 " 0.001 2.00e-02 2.50e+03 ... (remaining 752 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 911 2.78 - 3.31: 3769 3.31 - 3.84: 7051 3.84 - 4.37: 7661 4.37 - 4.90: 12927 Nonbonded interactions: 32319 Sorted by model distance: nonbonded pdb=" O PRO B 111 " pdb=" O HOH B 201 " model vdw 2.254 2.440 nonbonded pdb=" O LYS H 12 " pdb=" OG SER H 87 " model vdw 2.268 2.440 nonbonded pdb=" OG SER B 123 " pdb=" O HOH B 202 " model vdw 2.302 2.440 nonbonded pdb=" OG1 THR B 118 " pdb=" O HOH B 203 " model vdw 2.304 2.440 nonbonded pdb=" O VAL A 367 " pdb=" OG SER A 371 " model vdw 2.309 2.440 ... (remaining 32314 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.900 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: 9.970 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.900 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5619 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4273 Z= 0.255 Angle : 0.927 12.762 5805 Z= 0.479 Chirality : 0.058 0.424 616 Planarity : 0.006 0.067 755 Dihedral : 15.066 84.574 1507 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.76 % Favored : 90.06 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -3.24 (0.32), residues: 533 helix: -4.20 (0.65), residues: 30 sheet: -1.83 (0.42), residues: 144 loop : -2.21 (0.29), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.004 TRP B 36 HIS 0.006 0.004 HIS A 519 PHE 0.014 0.002 PHE B 27 TYR 0.022 0.002 TYR B 95 ARG 0.011 0.001 ARG A 355 *********************** 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 58 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.486 Fit side-chains REVERT: A 353 TRP cc_start: 0.4437 (p-90) cc_final: 0.4105 (p-90) REVERT: H 48 MET cc_start: 0.6276 (mpp) cc_final: 0.5899 (mpp) REVERT: B 83 MET cc_start: 0.7793 (mpp) cc_final: 0.7583 (mpp) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1571 time to fit residues: 11.7963 Evaluate side-chains 43 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 26 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 14 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5642 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4273 Z= 0.184 Angle : 0.655 9.483 5805 Z= 0.339 Chirality : 0.045 0.178 616 Planarity : 0.005 0.059 755 Dihedral : 5.976 27.833 599 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.38 % Favored : 90.43 % Rotamer: Outliers : 0.23 % Allowed : 7.24 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -3.27 (0.33), residues: 533 helix: -3.94 (0.69), residues: 32 sheet: -2.06 (0.39), residues: 154 loop : -2.12 (0.30), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 35 HIS 0.001 0.001 HIS A 519 PHE 0.025 0.002 PHE L 98 TYR 0.017 0.002 TYR A 505 ARG 0.004 0.001 ARG H 38 *********************** 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 54 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.482 Fit side-chains REVERT: L 98 PHE cc_start: 0.4820 (m-10) cc_final: 0.4236 (m-80) REVERT: B 34 MET cc_start: 0.6346 (mpp) cc_final: 0.5696 (tmm) outliers start: 1 outliers final: 0 residues processed: 54 average time/residue: 0.1313 time to fit residues: 9.6737 Evaluate side-chains 39 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 0.0980 chunk 32 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 0.0770 chunk 46 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 24 optimal weight: 0.0770 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5623 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4273 Z= 0.157 Angle : 0.621 9.310 5805 Z= 0.320 Chirality : 0.044 0.179 616 Planarity : 0.004 0.053 755 Dihedral : 5.681 27.098 599 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.94 % Favored : 89.87 % Rotamer: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -3.17 (0.33), residues: 533 helix: -3.68 (0.75), residues: 31 sheet: -1.87 (0.40), residues: 148 loop : -2.15 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 47 HIS 0.001 0.000 HIS A 519 PHE 0.019 0.002 PHE L 98 TYR 0.027 0.001 TYR A 449 ARG 0.003 0.000 ARG B 19 *********************** 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 56 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.479 Fit side-chains REVERT: H 48 MET cc_start: 0.6334 (mpp) cc_final: 0.6119 (mpp) REVERT: L 98 PHE cc_start: 0.4596 (m-80) cc_final: 0.4294 (m-80) REVERT: B 34 MET cc_start: 0.6213 (mpp) cc_final: 0.5960 (mtt) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1589 time to fit residues: 11.4984 Evaluate side-chains 38 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 chunk 31 optimal weight: 0.4980 chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 24 optimal weight: 0.1980 chunk 44 optimal weight: 0.0000 chunk 13 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5624 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 4273 Z= 0.148 Angle : 0.600 8.611 5805 Z= 0.308 Chirality : 0.044 0.181 616 Planarity : 0.004 0.051 755 Dihedral : 5.422 25.234 599 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.44 % Favored : 91.37 % Rotamer: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -3.11 (0.33), residues: 533 helix: -3.59 (0.75), residues: 31 sheet: -1.71 (0.40), residues: 143 loop : -2.18 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 47 HIS 0.001 0.001 HIS A 519 PHE 0.019 0.001 PHE L 98 TYR 0.020 0.001 TYR A 449 ARG 0.003 0.000 ARG B 19 *********************** 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 53 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.485 Fit side-chains REVERT: L 98 PHE cc_start: 0.4440 (m-80) cc_final: 0.4164 (m-80) REVERT: B 34 MET cc_start: 0.6352 (mpp) cc_final: 0.6022 (mtt) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1446 time to fit residues: 10.1544 Evaluate side-chains 39 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 5.9990 chunk 20 optimal weight: 0.3980 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 45 optimal weight: 0.0070 chunk 12 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 ASN A 481 ASN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5633 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4273 Z= 0.169 Angle : 0.627 10.340 5805 Z= 0.320 Chirality : 0.045 0.179 616 Planarity : 0.004 0.051 755 Dihedral : 5.663 26.554 599 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.51 % Favored : 89.31 % Rotamer: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -3.06 (0.33), residues: 533 helix: -3.17 (0.98), residues: 24 sheet: -1.98 (0.38), residues: 153 loop : -2.06 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.001 0.001 HIS A 519 PHE 0.016 0.002 PHE L 98 TYR 0.023 0.002 TYR A 449 ARG 0.004 0.001 ARG H 38 *********************** 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 56 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.508 Fit side-chains REVERT: A 351 TYR cc_start: 0.7450 (p90) cc_final: 0.7235 (p90) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1679 time to fit residues: 12.1071 Evaluate side-chains 38 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 23 optimal weight: 0.0170 chunk 4 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 5 optimal weight: 0.0970 chunk 28 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN H 1 GLN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5632 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4273 Z= 0.166 Angle : 0.630 10.022 5805 Z= 0.323 Chirality : 0.046 0.193 616 Planarity : 0.005 0.051 755 Dihedral : 5.611 26.391 599 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.94 % Favored : 89.87 % Rotamer: Outliers : 0.23 % Allowed : 4.75 % Favored : 95.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -3.02 (0.33), residues: 533 helix: -3.15 (0.98), residues: 24 sheet: -1.94 (0.38), residues: 155 loop : -2.03 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 36 HIS 0.001 0.001 HIS A 519 PHE 0.021 0.002 PHE L 98 TYR 0.019 0.002 TYR A 449 ARG 0.003 0.001 ARG B 19 *********************** 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 53 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.511 Fit side-chains REVERT: H 1 GLN cc_start: 0.5293 (OUTLIER) cc_final: 0.4596 (pp30) REVERT: H 27 TYR cc_start: 0.6188 (m-80) cc_final: 0.5711 (m-10) REVERT: H 37 VAL cc_start: 0.6853 (t) cc_final: 0.6567 (t) outliers start: 1 outliers final: 0 residues processed: 53 average time/residue: 0.1934 time to fit residues: 12.7969 Evaluate side-chains 38 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 50 optimal weight: 0.2980 chunk 31 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 0.0470 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 0.0000 chunk 34 optimal weight: 0.7980 overall best weight: 0.3082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN H 6 GLN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5615 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 4273 Z= 0.145 Angle : 0.609 6.949 5805 Z= 0.312 Chirality : 0.046 0.209 616 Planarity : 0.004 0.049 755 Dihedral : 5.366 25.500 599 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.32 % Favored : 89.68 % Rotamer: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -3.03 (0.33), residues: 533 helix: -3.48 (0.77), residues: 31 sheet: -1.84 (0.39), residues: 155 loop : -2.02 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 353 HIS 0.001 0.001 HIS A 519 PHE 0.012 0.001 PHE A 400 TYR 0.014 0.001 TYR A 449 ARG 0.003 0.000 ARG B 19 *********************** 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 53 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.484 Fit side-chains REVERT: A 351 TYR cc_start: 0.7481 (p90) cc_final: 0.7219 (p90) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1781 time to fit residues: 11.9486 Evaluate side-chains 37 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.7980 chunk 4 optimal weight: 0.0980 chunk 39 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 20 optimal weight: 0.2980 chunk 36 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5637 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4273 Z= 0.177 Angle : 0.649 11.300 5805 Z= 0.328 Chirality : 0.046 0.195 616 Planarity : 0.004 0.050 755 Dihedral : 5.608 26.023 599 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.26 % Favored : 88.74 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -3.11 (0.33), residues: 533 helix: -3.42 (0.78), residues: 31 sheet: -1.76 (0.39), residues: 143 loop : -2.17 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.001 0.001 HIS A 519 PHE 0.010 0.002 PHE A 486 TYR 0.019 0.002 TYR A 449 ARG 0.003 0.001 ARG H 38 *********************** 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 53 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.498 Fit side-chains REVERT: A 351 TYR cc_start: 0.7559 (p90) cc_final: 0.7209 (p90) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1982 time to fit residues: 13.1197 Evaluate side-chains 39 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 0.0980 chunk 44 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 0.0970 chunk 49 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5629 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 4273 Z= 0.158 Angle : 0.628 9.635 5805 Z= 0.317 Chirality : 0.046 0.214 616 Planarity : 0.004 0.050 755 Dihedral : 5.482 26.114 599 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -3.15 (0.33), residues: 533 helix: -3.72 (0.67), residues: 37 sheet: -1.86 (0.41), residues: 133 loop : -2.11 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.001 0.001 HIS A 519 PHE 0.010 0.002 PHE A 400 TYR 0.017 0.002 TYR A 449 ARG 0.003 0.001 ARG B 19 *********************** 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 53 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 351 TYR cc_start: 0.7587 (p90) cc_final: 0.7214 (p90) REVERT: B 2 GLU cc_start: 0.5528 (mp0) cc_final: 0.5105 (mp0) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1785 time to fit residues: 11.9683 Evaluate side-chains 43 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 32 optimal weight: 0.4980 chunk 43 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 17 optimal weight: 0.0970 chunk 42 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5634 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4273 Z= 0.185 Angle : 0.667 10.051 5805 Z= 0.338 Chirality : 0.047 0.203 616 Planarity : 0.005 0.050 755 Dihedral : 5.753 25.564 599 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.82 % Favored : 87.99 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -3.23 (0.32), residues: 533 helix: -3.69 (0.67), residues: 37 sheet: -1.94 (0.40), residues: 134 loop : -2.16 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP B 36 HIS 0.001 0.001 HIS A 519 PHE 0.012 0.002 PHE B 105 TYR 0.025 0.002 TYR A 421 ARG 0.003 0.001 ARG H 38 ********************** 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 53 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: A 351 TYR cc_start: 0.7462 (p90) cc_final: 0.7102 (p90) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1759 time to fit residues: 11.9024 Evaluate side-chains 40 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 0.0020 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 29 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 0.0170 chunk 1 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 overall best weight: 0.3826 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN ** L 3 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 = 0.3489 r_free = 0.3489 target = 0.050490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.041723 restraints weight = 37965.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.042879 restraints weight = 25616.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.043721 restraints weight = 18975.693| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5709 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4273 Z= 0.162 Angle : 0.640 8.555 5805 Z= 0.325 Chirality : 0.046 0.206 616 Planarity : 0.004 0.048 755 Dihedral : 5.576 25.465 599 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -3.12 (0.33), residues: 533 helix: -3.65 (0.69), residues: 37 sheet: -1.89 (0.40), residues: 134 loop : -2.07 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 353 HIS 0.001 0.001 HIS A 519 PHE 0.029 0.002 PHE L 98 TYR 0.023 0.002 TYR A 421 ARG 0.002 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1393.34 seconds wall clock time: 28 minutes 0.60 seconds (1680.60 seconds total)