Starting phenix.real_space_refine on Tue Feb 13 09:50:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y0w_33552/02_2024/7y0w_33552_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y0w_33552/02_2024/7y0w_33552.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y0w_33552/02_2024/7y0w_33552.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y0w_33552/02_2024/7y0w_33552.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y0w_33552/02_2024/7y0w_33552_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y0w_33552/02_2024/7y0w_33552_neut.pdb" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.023 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 22 5.16 5 C 3222 2.51 5 N 853 2.21 5 O 989 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 30": "NH1" <-> "NH2" Residue "A ASP 110": "OD1" <-> "OD2" Residue "B GLU 55": "OE1" <-> "OE2" Residue "B ARG 61": "NH1" <-> "NH2" Residue "B ARG 90": "NH1" <-> "NH2" Residue "B ASP 92": "OD1" <-> "OD2" Residue "B GLU 106": "OE1" <-> "OE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H ASP 23": "OD1" <-> "OD2" Residue "H ASP 54": "OD1" <-> "OD2" Residue "H ASP 90": "OD1" <-> "OD2" Residue "H GLU 99": "OE1" <-> "OE2" Residue "H ASP 108": "OD1" <-> "OD2" Residue "L GLU 72": "OE1" <-> "OE2" Residue "R GLU 340": "OE1" <-> "OE2" Residue "R PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 408": "NH1" <-> "NH2" Residue "R PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 471": "OE1" <-> "OE2" Residue "R PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 5086 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 930 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 6, 'TRANS': 116} Chain: "B" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 927 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 817 Classifications: {'peptide': 109} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "R" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1548 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 181} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "X" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.37, per 1000 atoms: 0.66 Number of scatterers: 5086 At special positions: 0 Unit cell: (102.96, 91.52, 83.2, 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 22 16.00 O 989 8.00 N 853 7.00 C 3222 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.06 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " 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 Links applied BETA1-4 " NAG X 1 " - " NAG X 2 " BETA1-6 " NAG X 1 " - " FUC X 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... Time building additional restraints: 1.93 Conformation dependent library (CDL) restraints added in 994.0 milliseconds 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1188 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 13 sheets defined 5.7% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.991A pdb=" N ILE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.789A pdb=" N ASP H 90 " --> pdb=" O LYS H 87 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.525A pdb=" N ASP L 84 " --> pdb=" O GLN L 81 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER L 85 " --> pdb=" O SER L 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 81 through 85' Processing helix chain 'R' and resid 349 through 353 removed outlier: 3.533A pdb=" N TRP R 353 " --> pdb=" O VAL R 350 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 371 removed outlier: 3.966A pdb=" N VAL R 367 " --> pdb=" O ASP R 364 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU R 368 " --> pdb=" O TYR R 365 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR R 369 " --> pdb=" O SER R 366 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASN R 370 " --> pdb=" O VAL R 367 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU R 371 " --> pdb=" O LEU R 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 364 through 371' Processing helix chain 'R' and resid 405 through 407 No H-bonds generated for 'chain 'R' and resid 405 through 407' Processing helix chain 'R' and resid 417 through 422 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.568A pdb=" N GLU A 10 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.568A pdb=" N GLU A 10 " --> pdb=" O THR A 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 5 through 7 removed outlier: 3.553A pdb=" N CYS B 23 " --> pdb=" O PHE B 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 Processing sheet with id=AA6, first strand: chain 'B' and resid 45 through 48 removed outlier: 5.559A pdb=" N LEU B 46 " --> pdb=" O GLN B 37 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLN B 37 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.239A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N CYS H 96 " --> pdb=" O GLY H 111 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.239A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.505A pdb=" N PHE L 73 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU L 72 " --> pdb=" O SER L 69 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER L 65 " --> pdb=" O THR L 76 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.156A pdb=" N LEU L 11 " --> pdb=" O GLU L 107 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR L 88 " --> pdb=" O THR L 104 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU L 35 " --> pdb=" O TYR L 51 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N TYR L 51 " --> pdb=" O LEU L 35 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 354 through 358 Processing sheet with id=AB3, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AB4, first strand: chain 'R' and resid 473 through 474 153 hydrogen bonds defined for protein. 372 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: 1.36 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 1635 1.35 - 1.48: 1497 1.48 - 1.62: 2055 1.62 - 1.76: 0 1.76 - 1.89: 28 Bond restraints: 5215 Sorted by residual: bond pdb=" CB CYS R 432 " pdb=" SG CYS R 432 " ideal model delta sigma weight residual 1.808 1.890 -0.082 3.30e-02 9.18e+02 6.24e+00 bond pdb=" CB LYS H 87 " pdb=" CG LYS H 87 " ideal model delta sigma weight residual 1.520 1.573 -0.053 3.00e-02 1.11e+03 3.12e+00 bond pdb=" CG LYS H 87 " pdb=" CD LYS H 87 " ideal model delta sigma weight residual 1.520 1.571 -0.051 3.00e-02 1.11e+03 2.85e+00 bond pdb=" CA ASP H 54 " pdb=" CB ASP H 54 " ideal model delta sigma weight residual 1.533 1.561 -0.028 1.66e-02 3.63e+03 2.82e+00 bond pdb=" CB GLN A 62 " pdb=" CG GLN A 62 " ideal model delta sigma weight residual 1.520 1.569 -0.049 3.00e-02 1.11e+03 2.70e+00 ... (remaining 5210 not shown) Histogram of bond angle deviations from ideal: 98.50 - 106.01: 125 106.01 - 113.51: 2741 113.51 - 121.02: 2485 121.02 - 128.52: 1700 128.52 - 136.02: 38 Bond angle restraints: 7089 Sorted by residual: angle pdb=" CA CYS R 379 " pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " ideal model delta sigma weight residual 114.40 129.59 -15.19 2.30e+00 1.89e-01 4.36e+01 angle pdb=" N CYS R 361 " pdb=" CA CYS R 361 " pdb=" C CYS R 361 " ideal model delta sigma weight residual 109.18 116.62 -7.44 1.42e+00 4.96e-01 2.74e+01 angle pdb=" CB LYS H 87 " pdb=" CG LYS H 87 " pdb=" CD LYS H 87 " ideal model delta sigma weight residual 111.30 123.07 -11.77 2.30e+00 1.89e-01 2.62e+01 angle pdb=" N CYS R 379 " pdb=" CA CYS R 379 " pdb=" C CYS R 379 " ideal model delta sigma weight residual 108.96 115.12 -6.16 1.49e+00 4.50e-01 1.71e+01 angle pdb=" C SER L 32 " pdb=" N THR L 33 " pdb=" CA THR L 33 " ideal model delta sigma weight residual 122.07 127.98 -5.91 1.43e+00 4.89e-01 1.71e+01 ... (remaining 7084 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 2761 17.38 - 34.76: 271 34.76 - 52.13: 49 52.13 - 69.51: 8 69.51 - 86.89: 8 Dihedral angle restraints: 3097 sinusoidal: 1227 harmonic: 1870 Sorted by residual: dihedral pdb=" CB CYS R 391 " pdb=" SG CYS R 391 " pdb=" SG CYS R 525 " pdb=" CB CYS R 525 " ideal model delta sinusoidal sigma weight residual 93.00 14.17 78.83 1 1.00e+01 1.00e-02 7.74e+01 dihedral pdb=" CA LEU A 99 " pdb=" C LEU A 99 " pdb=" N PHE A 100 " pdb=" CA PHE A 100 " ideal model delta harmonic sigma weight residual 180.00 -141.97 -38.03 0 5.00e+00 4.00e-02 5.78e+01 dihedral pdb=" CA CYS R 361 " pdb=" C CYS R 361 " pdb=" N VAL R 362 " pdb=" CA VAL R 362 " ideal model delta harmonic sigma weight residual 180.00 146.38 33.62 0 5.00e+00 4.00e-02 4.52e+01 ... (remaining 3094 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 694 0.098 - 0.196: 66 0.196 - 0.294: 9 0.294 - 0.393: 2 0.393 - 0.491: 1 Chirality restraints: 772 Sorted by residual: chirality pdb=" C1 FUC X 3 " pdb=" O6 NAG X 1 " pdb=" C2 FUC X 3 " pdb=" O5 FUC X 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 8.53e+00 chirality pdb=" CB ILE H 34 " pdb=" CA ILE H 34 " pdb=" CG1 ILE H 34 " pdb=" CG2 ILE H 34 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.49 2.00e-01 2.50e+01 6.02e+00 chirality pdb=" CB ILE H 51 " pdb=" CA ILE H 51 " pdb=" CG1 ILE H 51 " pdb=" CG2 ILE H 51 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 769 not shown) Planarity restraints: 915 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG X 1 " 0.107 2.00e-02 2.50e+03 8.85e-02 9.78e+01 pdb=" C7 NAG X 1 " -0.028 2.00e-02 2.50e+03 pdb=" C8 NAG X 1 " 0.081 2.00e-02 2.50e+03 pdb=" N2 NAG X 1 " -0.141 2.00e-02 2.50e+03 pdb=" O7 NAG X 1 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG X 2 " -0.059 2.00e-02 2.50e+03 4.85e-02 2.94e+01 pdb=" C7 NAG X 2 " 0.019 2.00e-02 2.50e+03 pdb=" C8 NAG X 2 " -0.046 2.00e-02 2.50e+03 pdb=" N2 NAG X 2 " 0.076 2.00e-02 2.50e+03 pdb=" O7 NAG X 2 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 107 " -0.049 5.00e-02 4.00e+02 7.50e-02 9.00e+00 pdb=" N PRO A 108 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 108 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 108 " -0.042 5.00e-02 4.00e+02 ... (remaining 912 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 1538 2.82 - 3.34: 3997 3.34 - 3.86: 8403 3.86 - 4.38: 9574 4.38 - 4.90: 17257 Nonbonded interactions: 40769 Sorted by model distance: nonbonded pdb=" OG SER R 469 " pdb=" OE1 GLU R 471 " model vdw 2.295 2.440 nonbonded pdb=" O GLY H 8 " pdb=" OG1 THR H 114 " model vdw 2.332 2.440 nonbonded pdb=" OE2 GLU R 406 " pdb=" OH TYR R 495 " model vdw 2.338 2.440 nonbonded pdb=" O ASN R 439 " pdb=" OG SER R 443 " model vdw 2.353 2.440 nonbonded pdb=" O SER A 107 " pdb=" OG SER A 107 " model vdw 2.359 2.440 ... (remaining 40764 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.520 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: 9.780 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.170 Find NCS groups from input model: 0.160 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 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 : 0.006 0.082 5215 Z= 0.400 Angle : 0.954 15.192 7089 Z= 0.514 Chirality : 0.062 0.491 772 Planarity : 0.008 0.088 915 Dihedral : 14.239 86.888 1888 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 0.18 % Allowed : 0.55 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -2.40 (0.32), residues: 641 helix: -4.93 (0.34), residues: 22 sheet: -1.28 (0.32), residues: 284 loop : -1.57 (0.30), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 36 HIS 0.006 0.002 HIS H 35 PHE 0.020 0.002 PHE R 347 TYR 0.030 0.002 TYR R 380 ARG 0.015 0.001 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 0.553 Fit side-chains REVERT: R 378 LYS cc_start: 0.7896 (ptpp) cc_final: 0.7673 (pttm) REVERT: R 390 LEU cc_start: 0.8148 (tp) cc_final: 0.7756 (tp) outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 0.1496 time to fit residues: 21.5405 Evaluate side-chains 92 residues out of total 547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN H 62 GLN H 112 GLN L 40 GLN R 370 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5215 Z= 0.278 Angle : 0.616 7.877 7089 Z= 0.329 Chirality : 0.048 0.250 772 Planarity : 0.005 0.061 915 Dihedral : 5.293 28.525 773 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.83 % Allowed : 11.54 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % 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: -2.17 (0.32), residues: 641 helix: -4.92 (0.37), residues: 22 sheet: -1.15 (0.31), residues: 289 loop : -1.37 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 96 HIS 0.004 0.001 HIS H 35 PHE 0.012 0.001 PHE R 347 TYR 0.017 0.001 TYR L 93 ARG 0.003 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 0.569 Fit side-chains REVERT: R 390 LEU cc_start: 0.8243 (tp) cc_final: 0.8034 (tp) outliers start: 10 outliers final: 9 residues processed: 96 average time/residue: 0.1484 time to fit residues: 19.0452 Evaluate side-chains 97 residues out of total 547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 88 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain R residue 336 CYS Chi-restraints excluded: chain R residue 349 SER Chi-restraints excluded: chain R residue 370 ASN Chi-restraints excluded: chain R residue 392 PHE Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 0.0980 chunk 17 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 50 optimal weight: 0.0070 chunk 55 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 45 optimal weight: 0.3980 overall best weight: 0.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5215 Z= 0.166 Angle : 0.544 6.687 7089 Z= 0.288 Chirality : 0.045 0.171 772 Planarity : 0.004 0.051 915 Dihedral : 4.890 29.216 773 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 1.65 % Allowed : 15.02 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % 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: -2.00 (0.33), residues: 641 helix: -5.05 (0.25), residues: 28 sheet: -0.86 (0.32), residues: 285 loop : -1.33 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 96 HIS 0.002 0.001 HIS H 27 PHE 0.010 0.001 PHE R 490 TYR 0.013 0.001 TYR R 369 ARG 0.006 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 0.492 Fit side-chains REVERT: H 87 LYS cc_start: 0.7905 (mmmt) cc_final: 0.7619 (tppt) REVERT: R 390 LEU cc_start: 0.8214 (tp) cc_final: 0.7986 (tp) outliers start: 9 outliers final: 6 residues processed: 93 average time/residue: 0.1449 time to fit residues: 18.4053 Evaluate side-chains 88 residues out of total 547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain R residue 336 CYS Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 392 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5215 Z= 0.261 Angle : 0.562 6.777 7089 Z= 0.298 Chirality : 0.046 0.210 772 Planarity : 0.004 0.055 915 Dihedral : 4.805 28.418 773 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.66 % Allowed : 15.93 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % 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: -1.96 (0.33), residues: 641 helix: -5.03 (0.23), residues: 28 sheet: -0.84 (0.32), residues: 290 loop : -1.31 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 96 HIS 0.003 0.001 HIS H 35 PHE 0.010 0.001 PHE B 73 TYR 0.016 0.001 TYR L 93 ARG 0.004 0.000 ARG L 26 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 86 time to evaluate : 0.529 Fit side-chains REVERT: H 87 LYS cc_start: 0.7914 (mmmt) cc_final: 0.7613 (tppt) REVERT: R 390 LEU cc_start: 0.8254 (tp) cc_final: 0.8045 (tp) outliers start: 20 outliers final: 16 residues processed: 99 average time/residue: 0.1449 time to fit residues: 19.2364 Evaluate side-chains 99 residues out of total 547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 83 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain R residue 336 CYS Chi-restraints excluded: chain R residue 349 SER Chi-restraints excluded: chain R residue 376 THR Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 392 PHE Chi-restraints excluded: chain R residue 428 ASP Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5215 Z= 0.264 Angle : 0.563 6.800 7089 Z= 0.297 Chirality : 0.046 0.202 772 Planarity : 0.004 0.052 915 Dihedral : 4.764 28.983 773 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 4.03 % Allowed : 15.93 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % 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: -1.91 (0.33), residues: 641 helix: -5.01 (0.23), residues: 28 sheet: -0.82 (0.32), residues: 292 loop : -1.26 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 96 HIS 0.004 0.001 HIS H 35 PHE 0.010 0.001 PHE A 95 TYR 0.016 0.001 TYR L 93 ARG 0.007 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 85 time to evaluate : 0.641 Fit side-chains REVERT: H 87 LYS cc_start: 0.7891 (mmmt) cc_final: 0.7600 (tppt) outliers start: 22 outliers final: 19 residues processed: 98 average time/residue: 0.1408 time to fit residues: 18.8131 Evaluate side-chains 103 residues out of total 547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 84 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain R residue 336 CYS Chi-restraints excluded: chain R residue 349 SER Chi-restraints excluded: chain R residue 376 THR Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 392 PHE Chi-restraints excluded: chain R residue 428 ASP Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 0.2980 chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 0.0670 chunk 4 optimal weight: 0.0870 chunk 19 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5215 Z= 0.189 Angle : 0.528 6.483 7089 Z= 0.279 Chirality : 0.045 0.173 772 Planarity : 0.004 0.051 915 Dihedral : 4.589 27.771 773 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.48 % Allowed : 17.95 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % 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: -1.87 (0.33), residues: 641 helix: -5.05 (0.22), residues: 28 sheet: -0.75 (0.32), residues: 291 loop : -1.27 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 96 HIS 0.003 0.001 HIS H 27 PHE 0.009 0.001 PHE A 100 TYR 0.013 0.001 TYR L 93 ARG 0.005 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 85 time to evaluate : 0.573 Fit side-chains REVERT: H 87 LYS cc_start: 0.7845 (mmmt) cc_final: 0.7572 (tppt) REVERT: H 112 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8199 (pt0) outliers start: 19 outliers final: 14 residues processed: 96 average time/residue: 0.1375 time to fit residues: 17.9393 Evaluate side-chains 99 residues out of total 547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain R residue 336 CYS Chi-restraints excluded: chain R residue 349 SER Chi-restraints excluded: chain R residue 376 THR Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 392 PHE Chi-restraints excluded: chain R residue 428 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 0.0000 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5215 Z= 0.278 Angle : 0.560 6.723 7089 Z= 0.294 Chirality : 0.046 0.197 772 Planarity : 0.004 0.052 915 Dihedral : 4.677 28.003 773 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.85 % Allowed : 17.95 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % 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: -1.85 (0.33), residues: 641 helix: -4.97 (0.26), residues: 28 sheet: -0.73 (0.31), residues: 291 loop : -1.26 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 96 HIS 0.004 0.001 HIS H 35 PHE 0.010 0.001 PHE A 95 TYR 0.017 0.001 TYR L 93 ARG 0.006 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 83 time to evaluate : 0.541 Fit side-chains REVERT: H 87 LYS cc_start: 0.7861 (mmmt) cc_final: 0.7586 (tppt) REVERT: H 112 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8230 (pt0) outliers start: 21 outliers final: 18 residues processed: 97 average time/residue: 0.1432 time to fit residues: 18.7690 Evaluate side-chains 101 residues out of total 547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain R residue 336 CYS Chi-restraints excluded: chain R residue 349 SER Chi-restraints excluded: chain R residue 376 THR Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 392 PHE Chi-restraints excluded: chain R residue 428 ASP Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.0070 chunk 46 optimal weight: 0.4980 chunk 54 optimal weight: 0.8980 chunk 57 optimal weight: 0.0170 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5215 Z= 0.183 Angle : 0.526 6.516 7089 Z= 0.276 Chirality : 0.045 0.209 772 Planarity : 0.004 0.050 915 Dihedral : 4.499 27.473 773 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 4.40 % Allowed : 17.95 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % 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: -1.58 (0.33), residues: 641 helix: -4.89 (0.33), residues: 22 sheet: -0.57 (0.32), residues: 280 loop : -1.13 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 96 HIS 0.003 0.001 HIS H 35 PHE 0.008 0.001 PHE A 100 TYR 0.012 0.001 TYR L 93 ARG 0.004 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 86 time to evaluate : 0.575 Fit side-chains REVERT: H 112 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8204 (pt0) REVERT: R 405 ASP cc_start: 0.7452 (t0) cc_final: 0.7231 (t0) outliers start: 24 outliers final: 22 residues processed: 99 average time/residue: 0.1335 time to fit residues: 18.0099 Evaluate side-chains 109 residues out of total 547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 86 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 44 GLN Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain R residue 336 CYS Chi-restraints excluded: chain R residue 349 SER Chi-restraints excluded: chain R residue 376 THR Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 391 CYS Chi-restraints excluded: chain R residue 392 PHE Chi-restraints excluded: chain R residue 428 ASP Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5215 Z= 0.272 Angle : 0.556 6.702 7089 Z= 0.293 Chirality : 0.046 0.217 772 Planarity : 0.004 0.052 915 Dihedral : 4.649 27.546 773 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 4.03 % Allowed : 18.50 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % 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: -1.57 (0.33), residues: 641 helix: -4.70 (0.46), residues: 22 sheet: -0.56 (0.32), residues: 281 loop : -1.14 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 96 HIS 0.003 0.001 HIS H 35 PHE 0.011 0.001 PHE A 95 TYR 0.017 0.001 TYR L 93 ARG 0.004 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 84 time to evaluate : 0.599 Fit side-chains REVERT: H 112 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8255 (pt0) outliers start: 22 outliers final: 19 residues processed: 97 average time/residue: 0.1425 time to fit residues: 18.9364 Evaluate side-chains 102 residues out of total 547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 82 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain R residue 336 CYS Chi-restraints excluded: chain R residue 349 SER Chi-restraints excluded: chain R residue 376 THR Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 391 CYS Chi-restraints excluded: chain R residue 392 PHE Chi-restraints excluded: chain R residue 428 ASP Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 5 optimal weight: 0.0870 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5215 Z= 0.210 Angle : 0.536 6.607 7089 Z= 0.282 Chirality : 0.045 0.194 772 Planarity : 0.004 0.050 915 Dihedral : 4.554 27.635 773 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.66 % Allowed : 18.86 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % 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: -1.50 (0.33), residues: 641 helix: -4.58 (0.53), residues: 22 sheet: -0.50 (0.32), residues: 280 loop : -1.12 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 96 HIS 0.003 0.001 HIS H 35 PHE 0.008 0.001 PHE A 100 TYR 0.014 0.001 TYR L 93 ARG 0.004 0.000 ARG L 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 80 time to evaluate : 0.512 Fit side-chains REVERT: H 112 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8226 (pt0) outliers start: 20 outliers final: 19 residues processed: 91 average time/residue: 0.1401 time to fit residues: 17.3790 Evaluate side-chains 100 residues out of total 547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 80 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain R residue 336 CYS Chi-restraints excluded: chain R residue 349 SER Chi-restraints excluded: chain R residue 376 THR Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 391 CYS Chi-restraints excluded: chain R residue 392 PHE Chi-restraints excluded: chain R residue 428 ASP Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 50 optimal weight: 0.0770 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.124422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.101129 restraints weight = 6676.523| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.95 r_work: 0.2958 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5215 Z= 0.226 Angle : 0.543 6.583 7089 Z= 0.284 Chirality : 0.046 0.199 772 Planarity : 0.004 0.051 915 Dihedral : 4.561 27.239 773 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 4.03 % Allowed : 18.68 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % 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: -1.50 (0.33), residues: 641 helix: -4.49 (0.59), residues: 22 sheet: -0.52 (0.32), residues: 280 loop : -1.10 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 96 HIS 0.004 0.001 HIS H 35 PHE 0.009 0.001 PHE A 95 TYR 0.015 0.001 TYR L 93 ARG 0.004 0.000 ARG L 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1580.61 seconds wall clock time: 29 minutes 11.87 seconds (1751.87 seconds total)