Starting phenix.real_space_refine on Fri Jul 19 02:31:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tld_41367/07_2024/8tld_41367.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tld_41367/07_2024/8tld_41367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tld_41367/07_2024/8tld_41367.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tld_41367/07_2024/8tld_41367.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tld_41367/07_2024/8tld_41367.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tld_41367/07_2024/8tld_41367.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 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 27 5.16 5 C 3776 2.51 5 N 1040 2.21 5 O 1139 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 385": "OD1" <-> "OD2" Residue "F ASP 166": "OD1" <-> "OD2" Residue "F PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 237": "OD1" <-> "OD2" Residue "F ASP 271": "OD1" <-> "OD2" Residue "F ASP 299": "OD1" <-> "OD2" Residue "F GLU 318": "OE1" <-> "OE2" Residue "F GLU 324": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 5982 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 758 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 9, 'TRANS': 84} Chain breaks: 1 Chain: "C" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 862 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain: "D" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 879 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "E" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 942 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "F" Number of atoms: 2471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2471 Classifications: {'peptide': 308} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 291} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.93, per 1000 atoms: 0.66 Number of scatterers: 5982 At special positions: 0 Unit cell: (80.972, 112.316, 124.07, 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 27 16.00 O 1139 8.00 N 1040 7.00 C 3776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 45 " distance=2.03 Simple disulfide: pdb=" SG CYS B 72 " - pdb=" SG CYS B 93 " distance=2.03 Simple disulfide: pdb=" SG CYS B 83 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS D 106 " distance=2.03 Simple disulfide: pdb=" SG CYS C 106 " - pdb=" SG CYS D 64 " distance=2.03 Simple disulfide: pdb=" SG CYS F 134 " - pdb=" SG CYS F 155 " distance=2.03 Simple disulfide: pdb=" SG CYS F 182 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 269 " - pdb=" SG CYS F 316 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C 200 " - " ASN C 48 " " NAG F 501 " - " ASN F 35 " " NAG F 502 " - " ASN F 131 " " NAG F 503 " - " ASN F 216 " " NAG F 504 " - " ASN F 244 " Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 1.1 seconds 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1400 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 11 sheets defined 24.9% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'B' and resid 27 through 33 Processing helix chain 'B' and resid 51 through 55 removed outlier: 3.859A pdb=" N ARG B 55 " --> pdb=" O GLN B 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 51 through 55' Processing helix chain 'C' and resid 26 through 41 Processing helix chain 'C' and resid 41 through 46 Processing helix chain 'C' and resid 64 through 78 Processing helix chain 'C' and resid 84 through 105 removed outlier: 3.673A pdb=" N ASN C 91 " --> pdb=" O ARG C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 130 Processing helix chain 'D' and resid 29 through 41 Processing helix chain 'D' and resid 41 through 46 removed outlier: 3.536A pdb=" N LEU D 45 " --> pdb=" O HIS D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 63 removed outlier: 3.721A pdb=" N LEU D 63 " --> pdb=" O ASN D 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 60 through 63' Processing helix chain 'D' and resid 64 through 79 Processing helix chain 'D' and resid 83 through 106 removed outlier: 4.037A pdb=" N ARG D 87 " --> pdb=" O GLY D 83 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR D 98 " --> pdb=" O LEU D 94 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE D 99 " --> pdb=" O ILE D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 130 Processing helix chain 'E' and resid 382 through 386 Processing helix chain 'F' and resid 232 through 237 Processing sheet with id=AA1, first strand: chain 'B' and resid 34 through 37 Processing sheet with id=AA2, first strand: chain 'B' and resid 59 through 64 Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 55 removed outlier: 4.293A pdb=" N GLU D 109 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SER F 95 " --> pdb=" O ASN F 70 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 53 through 55 removed outlier: 4.293A pdb=" N GLU D 109 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SER F 95 " --> pdb=" O ASN F 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 344 through 350 Processing sheet with id=AA6, first strand: chain 'E' and resid 387 through 392 Processing sheet with id=AA7, first strand: chain 'F' and resid 34 through 42 removed outlier: 5.518A pdb=" N ASN F 35 " --> pdb=" O LYS F 51 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LYS F 51 " --> pdb=" O ASN F 35 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS F 39 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR F 41 " --> pdb=" O GLN F 45 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLN F 45 " --> pdb=" O THR F 41 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 130 through 140 removed outlier: 5.696A pdb=" N ASN F 131 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU F 158 " --> pdb=" O ASN F 131 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL F 151 " --> pdb=" O ARG F 200 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ARG F 200 " --> pdb=" O VAL F 151 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ILE F 194 " --> pdb=" O TRP F 157 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N SER F 186 " --> pdb=" O ILE F 194 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 178 through 181 Processing sheet with id=AB1, first strand: chain 'F' and resid 246 through 250 Processing sheet with id=AB2, first strand: chain 'F' and resid 284 through 289 280 hydrogen bonds defined for protein. 768 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: 1.65 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1954 1.34 - 1.46: 1304 1.46 - 1.58: 2820 1.58 - 1.70: 2 1.70 - 1.82: 36 Bond restraints: 6116 Sorted by residual: bond pdb=" CG PRO C 54 " pdb=" CD PRO C 54 " ideal model delta sigma weight residual 1.503 1.296 0.207 3.40e-02 8.65e+02 3.70e+01 bond pdb=" CB PRO C 54 " pdb=" CG PRO C 54 " ideal model delta sigma weight residual 1.492 1.668 -0.176 5.00e-02 4.00e+02 1.23e+01 bond pdb=" N PRO C 54 " pdb=" CD PRO C 54 " ideal model delta sigma weight residual 1.473 1.522 -0.049 1.40e-02 5.10e+03 1.21e+01 bond pdb=" N PRO C 54 " pdb=" CA PRO C 54 " ideal model delta sigma weight residual 1.469 1.438 0.030 1.28e-02 6.10e+03 5.64e+00 bond pdb=" C1 NAG F 503 " pdb=" O5 NAG F 503 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.14e+00 ... (remaining 6111 not shown) Histogram of bond angle deviations from ideal: 90.46 - 99.17: 4 99.17 - 107.89: 274 107.89 - 116.60: 4178 116.60 - 125.31: 3717 125.31 - 134.03: 135 Bond angle restraints: 8308 Sorted by residual: angle pdb=" CA PRO C 54 " pdb=" N PRO C 54 " pdb=" CD PRO C 54 " ideal model delta sigma weight residual 112.00 93.99 18.01 1.40e+00 5.10e-01 1.65e+02 angle pdb=" N PRO C 54 " pdb=" CD PRO C 54 " pdb=" CG PRO C 54 " ideal model delta sigma weight residual 103.20 90.46 12.74 1.50e+00 4.44e-01 7.21e+01 angle pdb=" CA PRO C 54 " pdb=" CB PRO C 54 " pdb=" CG PRO C 54 " ideal model delta sigma weight residual 104.50 94.84 9.66 1.90e+00 2.77e-01 2.59e+01 angle pdb=" CA PRO F 261 " pdb=" N PRO F 261 " pdb=" CD PRO F 261 " ideal model delta sigma weight residual 112.00 106.01 5.99 1.40e+00 5.10e-01 1.83e+01 angle pdb=" C GLU D 24 " pdb=" N ILE D 25 " pdb=" CA ILE D 25 " ideal model delta sigma weight residual 122.13 129.53 -7.40 1.85e+00 2.92e-01 1.60e+01 ... (remaining 8303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 3192 17.71 - 35.41: 429 35.41 - 53.12: 121 53.12 - 70.82: 18 70.82 - 88.53: 12 Dihedral angle restraints: 3772 sinusoidal: 1622 harmonic: 2150 Sorted by residual: dihedral pdb=" CA GLN C 102 " pdb=" C GLN C 102 " pdb=" N LYS C 103 " pdb=" CA LYS C 103 " ideal model delta harmonic sigma weight residual 180.00 152.91 27.09 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA ASN C 48 " pdb=" C ASN C 48 " pdb=" N GLU C 49 " pdb=" CA GLU C 49 " ideal model delta harmonic sigma weight residual -180.00 -154.26 -25.74 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CB CYS C 64 " pdb=" SG CYS C 64 " pdb=" SG CYS D 106 " pdb=" CB CYS D 106 " ideal model delta sinusoidal sigma weight residual -86.00 -45.06 -40.94 1 1.00e+01 1.00e-02 2.35e+01 ... (remaining 3769 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 874 0.084 - 0.167: 70 0.167 - 0.251: 1 0.251 - 0.334: 0 0.334 - 0.418: 1 Chirality restraints: 946 Sorted by residual: chirality pdb=" C1 NAG C 200 " pdb=" ND2 ASN C 48 " pdb=" C2 NAG C 200 " pdb=" O5 NAG C 200 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.36e+00 chirality pdb=" CA ASN D 60 " pdb=" N ASN D 60 " pdb=" C ASN D 60 " pdb=" CB ASN D 60 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" C1 NAG F 501 " pdb=" ND2 ASN F 35 " pdb=" C2 NAG F 501 " pdb=" O5 NAG F 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 6.89e-01 ... (remaining 943 not shown) Planarity restraints: 1059 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 53 " -0.102 5.00e-02 4.00e+02 1.39e-01 3.07e+01 pdb=" N PRO C 54 " 0.239 5.00e-02 4.00e+02 pdb=" CA PRO C 54 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO C 54 " -0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 110 " -0.371 9.50e-02 1.11e+02 1.67e-01 1.80e+01 pdb=" NE ARG C 110 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG C 110 " 0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG C 110 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 110 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS F 260 " 0.063 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO F 261 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO F 261 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO F 261 " 0.050 5.00e-02 4.00e+02 ... (remaining 1056 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 343 2.72 - 3.27: 5661 3.27 - 3.81: 9630 3.81 - 4.36: 11263 4.36 - 4.90: 19145 Nonbonded interactions: 46042 Sorted by model distance: nonbonded pdb=" O PRO E 343 " pdb=" OG SER E 429 " model vdw 2.181 2.440 nonbonded pdb=" OG1 THR D 34 " pdb=" OD1 ASN D 91 " model vdw 2.183 2.440 nonbonded pdb=" OD2 ASP B 104 " pdb=" NH1 ARG C 87 " model vdw 2.185 2.520 nonbonded pdb=" NZ LYS F 260 " pdb=" O PHE F 265 " model vdw 2.198 2.520 nonbonded pdb=" O THR C 50 " pdb=" NH1 ARG C 52 " model vdw 2.211 2.520 ... (remaining 46037 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and resid 25 through 131) selection = (chain 'D' and resid 25 through 131) } 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: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.290 Find NCS groups from input model: 0.120 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.207 6116 Z= 0.303 Angle : 0.732 18.009 8308 Z= 0.407 Chirality : 0.045 0.418 946 Planarity : 0.009 0.167 1054 Dihedral : 17.428 88.526 2348 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.76 % Favored : 95.83 % Rotamer: Outliers : 0.60 % Allowed : 24.13 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.32), residues: 719 helix: 0.48 (0.41), residues: 169 sheet: 0.65 (0.36), residues: 226 loop : -0.96 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 322 HIS 0.006 0.001 HIS C 61 PHE 0.024 0.002 PHE D 116 TYR 0.009 0.001 TYR F 172 ARG 0.018 0.001 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 126 time to evaluate : 0.686 Fit side-chains revert: symmetry clash REVERT: D 123 PHE cc_start: 0.7327 (t80) cc_final: 0.6906 (t80) REVERT: F 186 SER cc_start: 0.8080 (m) cc_final: 0.7838 (p) REVERT: F 292 ASN cc_start: 0.7951 (OUTLIER) cc_final: 0.6940 (t0) REVERT: F 324 GLU cc_start: 0.7743 (tp30) cc_final: 0.7373 (tp30) outliers start: 4 outliers final: 0 residues processed: 127 average time/residue: 0.2050 time to fit residues: 33.0920 Evaluate side-chains 124 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 292 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 0.0570 chunk 29 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 54 optimal weight: 0.0050 chunk 21 optimal weight: 0.4980 chunk 33 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.3912 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.0796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 6116 Z= 0.197 Angle : 0.571 6.030 8308 Z= 0.299 Chirality : 0.044 0.374 946 Planarity : 0.006 0.081 1054 Dihedral : 6.540 56.837 903 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.06 % Favored : 96.52 % Rotamer: Outliers : 3.32 % Allowed : 22.78 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.32), residues: 719 helix: 0.83 (0.41), residues: 164 sheet: 0.81 (0.36), residues: 227 loop : -0.75 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 322 HIS 0.004 0.001 HIS F 277 PHE 0.012 0.002 PHE F 198 TYR 0.011 0.001 TYR F 272 ARG 0.006 0.000 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 132 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 54 PRO cc_start: 0.6932 (Cg_exo) cc_final: 0.6696 (Cg_endo) REVERT: F 40 VAL cc_start: 0.8292 (t) cc_final: 0.8069 (m) REVERT: F 292 ASN cc_start: 0.7988 (OUTLIER) cc_final: 0.7028 (t0) REVERT: F 309 ARG cc_start: 0.6757 (mtp180) cc_final: 0.6551 (mtp180) REVERT: F 324 GLU cc_start: 0.7734 (tp30) cc_final: 0.7402 (tp30) outliers start: 22 outliers final: 10 residues processed: 142 average time/residue: 0.2148 time to fit residues: 38.3492 Evaluate side-chains 139 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 292 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 43 optimal weight: 0.4980 chunk 17 optimal weight: 0.8980 chunk 63 optimal weight: 0.0970 chunk 68 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 102 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 6116 Z= 0.216 Angle : 0.562 6.386 8308 Z= 0.292 Chirality : 0.043 0.345 946 Planarity : 0.005 0.063 1054 Dihedral : 6.367 57.929 903 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.48 % Favored : 96.11 % Rotamer: Outliers : 4.52 % Allowed : 22.17 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.32), residues: 719 helix: 0.90 (0.41), residues: 164 sheet: 0.71 (0.35), residues: 230 loop : -0.76 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 322 HIS 0.004 0.001 HIS F 106 PHE 0.014 0.002 PHE F 198 TYR 0.010 0.001 TYR E 376 ARG 0.003 0.000 ARG E 327 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 124 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.8261 (m) REVERT: F 40 VAL cc_start: 0.8352 (t) cc_final: 0.8144 (m) REVERT: F 240 ASN cc_start: 0.8046 (m-40) cc_final: 0.7808 (m-40) REVERT: F 292 ASN cc_start: 0.8056 (OUTLIER) cc_final: 0.7110 (t0) REVERT: F 322 TRP cc_start: 0.7872 (m100) cc_final: 0.7609 (m-10) outliers start: 30 outliers final: 15 residues processed: 138 average time/residue: 0.2048 time to fit residues: 35.9376 Evaluate side-chains 141 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 124 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 131 TRP Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain F residue 218 SER Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 292 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 6116 Z= 0.326 Angle : 0.636 7.142 8308 Z= 0.328 Chirality : 0.045 0.339 946 Planarity : 0.006 0.058 1054 Dihedral : 6.464 57.780 903 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.01 % Favored : 94.58 % Rotamer: Outliers : 4.68 % Allowed : 23.38 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.32), residues: 719 helix: 0.62 (0.40), residues: 169 sheet: 0.53 (0.35), residues: 230 loop : -0.93 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 322 HIS 0.007 0.002 HIS F 106 PHE 0.021 0.002 PHE F 198 TYR 0.017 0.002 TYR E 376 ARG 0.007 0.001 ARG C 112 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 139 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7617 (tp) REVERT: D 123 PHE cc_start: 0.7360 (t80) cc_final: 0.7126 (t80) REVERT: E 421 TYR cc_start: 0.8430 (m-80) cc_final: 0.7840 (m-80) REVERT: F 40 VAL cc_start: 0.8390 (t) cc_final: 0.8180 (m) REVERT: F 88 THR cc_start: 0.7338 (t) cc_final: 0.6588 (m) REVERT: F 186 SER cc_start: 0.8216 (m) cc_final: 0.7986 (p) REVERT: F 292 ASN cc_start: 0.8120 (OUTLIER) cc_final: 0.7206 (t0) REVERT: F 322 TRP cc_start: 0.7974 (m100) cc_final: 0.7570 (m-10) outliers start: 31 outliers final: 20 residues processed: 153 average time/residue: 0.2030 time to fit residues: 39.3815 Evaluate side-chains 155 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 131 TRP Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 433 SER Chi-restraints excluded: chain F residue 39 LYS Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain F residue 218 SER Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 292 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 6116 Z= 0.242 Angle : 0.580 6.904 8308 Z= 0.298 Chirality : 0.044 0.325 946 Planarity : 0.005 0.063 1054 Dihedral : 6.325 57.538 903 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.76 % Favored : 95.83 % Rotamer: Outliers : 5.58 % Allowed : 23.38 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.31), residues: 719 helix: 0.74 (0.40), residues: 169 sheet: 0.48 (0.35), residues: 230 loop : -0.88 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 322 HIS 0.005 0.001 HIS C 61 PHE 0.014 0.002 PHE F 198 TYR 0.012 0.001 TYR E 376 ARG 0.004 0.000 ARG F 59 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 120 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 VAL cc_start: 0.8253 (t) cc_final: 0.7993 (p) REVERT: C 84 THR cc_start: 0.8542 (OUTLIER) cc_final: 0.8267 (m) REVERT: D 123 PHE cc_start: 0.7392 (t80) cc_final: 0.7109 (t80) REVERT: E 421 TYR cc_start: 0.8432 (m-80) cc_final: 0.7762 (m-80) REVERT: F 186 SER cc_start: 0.8194 (m) cc_final: 0.7981 (p) REVERT: F 193 ASN cc_start: 0.7822 (m110) cc_final: 0.7619 (m-40) REVERT: F 322 TRP cc_start: 0.7875 (m100) cc_final: 0.7459 (m-10) outliers start: 37 outliers final: 27 residues processed: 140 average time/residue: 0.1938 time to fit residues: 34.9153 Evaluate side-chains 144 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 116 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 131 TRP Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 433 SER Chi-restraints excluded: chain F residue 39 LYS Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 131 ASN Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain F residue 218 SER Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain F residue 289 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 chunk 35 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 6116 Z= 0.295 Angle : 0.637 11.752 8308 Z= 0.328 Chirality : 0.044 0.327 946 Planarity : 0.005 0.063 1054 Dihedral : 6.365 57.000 901 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.01 % Favored : 94.58 % Rotamer: Outliers : 5.58 % Allowed : 23.23 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.31), residues: 719 helix: 0.76 (0.40), residues: 169 sheet: 0.34 (0.34), residues: 232 loop : -0.99 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 322 HIS 0.005 0.001 HIS F 106 PHE 0.018 0.002 PHE F 198 TYR 0.014 0.002 TYR E 376 ARG 0.005 0.001 ARG F 174 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 123 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 THR cc_start: 0.8551 (OUTLIER) cc_final: 0.8279 (m) REVERT: D 123 PHE cc_start: 0.7340 (t80) cc_final: 0.7035 (t80) REVERT: E 421 TYR cc_start: 0.8455 (m-80) cc_final: 0.7731 (m-80) REVERT: F 186 SER cc_start: 0.8214 (m) cc_final: 0.7966 (p) REVERT: F 193 ASN cc_start: 0.7867 (m110) cc_final: 0.7639 (m110) REVERT: F 220 LYS cc_start: 0.7108 (OUTLIER) cc_final: 0.6823 (pttt) outliers start: 37 outliers final: 29 residues processed: 143 average time/residue: 0.1943 time to fit residues: 35.5510 Evaluate side-chains 151 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 120 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 85 HIS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 131 TRP Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 433 SER Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain F residue 218 SER Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain F residue 289 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 3.9990 chunk 57 optimal weight: 0.2980 chunk 37 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 20 optimal weight: 6.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 6116 Z= 0.203 Angle : 0.585 9.480 8308 Z= 0.299 Chirality : 0.044 0.321 946 Planarity : 0.005 0.064 1054 Dihedral : 6.359 57.589 901 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.20 % Favored : 96.38 % Rotamer: Outliers : 4.83 % Allowed : 23.98 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.31), residues: 719 helix: 0.89 (0.40), residues: 169 sheet: 0.48 (0.34), residues: 228 loop : -0.89 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 322 HIS 0.004 0.001 HIS C 61 PHE 0.013 0.002 PHE F 198 TYR 0.011 0.001 TYR F 172 ARG 0.006 0.000 ARG F 174 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 119 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 VAL cc_start: 0.8145 (t) cc_final: 0.7873 (p) REVERT: C 84 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.8245 (m) REVERT: D 123 PHE cc_start: 0.7377 (t80) cc_final: 0.7016 (t80) REVERT: E 421 TYR cc_start: 0.8467 (m-80) cc_final: 0.7749 (m-80) REVERT: F 193 ASN cc_start: 0.7817 (m110) cc_final: 0.7581 (m110) outliers start: 32 outliers final: 24 residues processed: 134 average time/residue: 0.1891 time to fit residues: 32.9217 Evaluate side-chains 142 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 85 HIS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 131 TRP Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain F residue 289 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 53 optimal weight: 0.0570 chunk 61 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 6116 Z= 0.197 Angle : 0.579 8.658 8308 Z= 0.295 Chirality : 0.043 0.327 946 Planarity : 0.005 0.062 1054 Dihedral : 6.280 57.511 901 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.17 % Favored : 95.41 % Rotamer: Outliers : 4.83 % Allowed : 24.59 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.32), residues: 719 helix: 0.89 (0.40), residues: 169 sheet: 0.55 (0.35), residues: 228 loop : -0.83 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 50 HIS 0.004 0.001 HIS C 61 PHE 0.014 0.002 PHE F 198 TYR 0.009 0.001 TYR E 376 ARG 0.006 0.000 ARG F 174 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 122 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 VAL cc_start: 0.8133 (t) cc_final: 0.7884 (p) REVERT: C 84 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.8235 (m) REVERT: D 42 ARG cc_start: 0.6405 (OUTLIER) cc_final: 0.5479 (ttm110) REVERT: D 123 PHE cc_start: 0.7333 (t80) cc_final: 0.7064 (t80) REVERT: E 421 TYR cc_start: 0.8461 (m-80) cc_final: 0.7734 (m-80) REVERT: F 193 ASN cc_start: 0.7763 (m110) cc_final: 0.7547 (m110) outliers start: 32 outliers final: 24 residues processed: 140 average time/residue: 0.1997 time to fit residues: 35.5995 Evaluate side-chains 144 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 118 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 85 HIS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 289 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 0.3980 chunk 59 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 6116 Z= 0.220 Angle : 0.604 9.796 8308 Z= 0.303 Chirality : 0.043 0.331 946 Planarity : 0.005 0.061 1054 Dihedral : 6.292 57.119 901 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.62 % Favored : 95.97 % Rotamer: Outliers : 4.22 % Allowed : 25.64 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.32), residues: 719 helix: 0.92 (0.40), residues: 169 sheet: 0.48 (0.34), residues: 229 loop : -0.86 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 322 HIS 0.004 0.001 HIS C 61 PHE 0.015 0.002 PHE F 198 TYR 0.012 0.001 TYR F 172 ARG 0.006 0.000 ARG F 174 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 122 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 VAL cc_start: 0.8145 (t) cc_final: 0.7892 (p) REVERT: C 84 THR cc_start: 0.8536 (OUTLIER) cc_final: 0.8270 (m) REVERT: D 42 ARG cc_start: 0.6451 (OUTLIER) cc_final: 0.5724 (ttm110) REVERT: D 123 PHE cc_start: 0.7322 (t80) cc_final: 0.7052 (t80) REVERT: E 421 TYR cc_start: 0.8497 (m-80) cc_final: 0.7788 (m-80) outliers start: 28 outliers final: 24 residues processed: 139 average time/residue: 0.1925 time to fit residues: 34.3163 Evaluate side-chains 147 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 121 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 85 HIS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 433 SER Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 289 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 0.2980 chunk 64 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 5 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 331 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 6116 Z= 0.243 Angle : 0.624 8.861 8308 Z= 0.312 Chirality : 0.044 0.334 946 Planarity : 0.005 0.061 1054 Dihedral : 6.355 56.845 901 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.17 % Favored : 95.41 % Rotamer: Outliers : 4.83 % Allowed : 24.74 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.32), residues: 719 helix: 0.95 (0.41), residues: 169 sheet: 0.44 (0.35), residues: 229 loop : -0.89 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 434 HIS 0.004 0.001 HIS C 61 PHE 0.018 0.002 PHE F 198 TYR 0.013 0.002 TYR F 173 ARG 0.006 0.000 ARG F 174 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 121 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8300 (m) REVERT: D 42 ARG cc_start: 0.6528 (OUTLIER) cc_final: 0.5720 (ttm110) REVERT: D 123 PHE cc_start: 0.7329 (t80) cc_final: 0.7064 (t80) REVERT: E 421 TYR cc_start: 0.8525 (m-80) cc_final: 0.7779 (m-80) REVERT: F 45 GLN cc_start: 0.7320 (tt0) cc_final: 0.6874 (mt0) REVERT: F 193 ASN cc_start: 0.7788 (m110) cc_final: 0.7521 (m110) outliers start: 32 outliers final: 23 residues processed: 142 average time/residue: 0.1928 time to fit residues: 35.0672 Evaluate side-chains 144 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 119 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 85 HIS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 433 SER Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 326 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 40 optimal weight: 0.0670 chunk 63 optimal weight: 0.0980 chunk 37 optimal weight: 0.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.149865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.132860 restraints weight = 9532.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.135878 restraints weight = 5860.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.137909 restraints weight = 4038.787| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6116 Z= 0.194 Angle : 0.614 10.612 8308 Z= 0.305 Chirality : 0.044 0.334 946 Planarity : 0.005 0.062 1054 Dihedral : 6.328 57.330 901 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.06 % Favored : 96.52 % Rotamer: Outliers : 4.07 % Allowed : 25.19 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.32), residues: 719 helix: 1.02 (0.41), residues: 169 sheet: 0.63 (0.35), residues: 224 loop : -0.81 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 434 HIS 0.006 0.001 HIS D 61 PHE 0.014 0.002 PHE F 198 TYR 0.013 0.001 TYR F 172 ARG 0.006 0.000 ARG F 174 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1577.93 seconds wall clock time: 28 minutes 50.20 seconds (1730.20 seconds total)