Starting phenix.real_space_refine on Tue Feb 13 12:46:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dl8_27499/02_2024/8dl8_27499.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dl8_27499/02_2024/8dl8_27499.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dl8_27499/02_2024/8dl8_27499.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dl8_27499/02_2024/8dl8_27499.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dl8_27499/02_2024/8dl8_27499.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dl8_27499/02_2024/8dl8_27499.pdb" } resolution = 3.0 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= 0.002 sd= 0.062 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: 5 Type Number sf(0) Gaussians Co 2 6.85 5 S 34 5.16 5 C 3969 2.51 5 N 1049 2.21 5 O 1154 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 128": "OE1" <-> "OE2" Residue "D TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6208 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3387 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 433} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1373 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 203} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 290 Unresolved non-hydrogen angles: 372 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 154 Chain: "D" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1445 Classifications: {'peptide': 219} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 79} Link IDs: {'PTRANS': 14, 'TRANS': 204} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 326 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 91 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2052 SG CYS A 326 23.364 42.046 35.119 1.00104.32 S Time building chain proxies: 4.23, per 1000 atoms: 0.68 Number of scatterers: 6208 At special positions: 0 Unit cell: (73.44, 74.52, 145.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Co 2 26.99 S 34 16.00 O 1154 8.00 N 1049 7.00 C 3969 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 553 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 108 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 115 " 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 Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 1.5 seconds 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1604 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 8 sheets defined 49.0% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 15 through 23 Processing helix chain 'A' and resid 23 through 54 Processing helix chain 'A' and resid 57 through 85 removed outlier: 3.745A pdb=" N THR A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ALA A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ILE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 removed outlier: 3.563A pdb=" N HIS A 116 " --> pdb=" O MET A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 123 Processing helix chain 'A' and resid 126 through 156 removed outlier: 3.597A pdb=" N ARG A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 164 Processing helix chain 'A' and resid 166 through 199 Proline residue: A 189 - end of helix Processing helix chain 'A' and resid 200 through 230 Processing helix chain 'A' and resid 231 through 234 removed outlier: 3.740A pdb=" N ALA A 234 " --> pdb=" O PRO A 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 231 through 234' Processing helix chain 'A' and resid 285 through 305 removed outlier: 4.667A pdb=" N GLU A 290 " --> pdb=" O SER A 286 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing helix chain 'A' and resid 307 through 317 Processing helix chain 'A' and resid 326 through 335 removed outlier: 4.262A pdb=" N GLY A 330 " --> pdb=" O CYS A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 367 Processing helix chain 'A' and resid 368 through 392 removed outlier: 3.748A pdb=" N PHE A 392 " --> pdb=" O VAL A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 483 Processing helix chain 'A' and resid 488 through 514 Processing helix chain 'A' and resid 519 through 547 Processing helix chain 'C' and resid 99 through 103 removed outlier: 4.052A pdb=" N LEU C 103 " --> pdb=" O SER C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 147 Processing helix chain 'C' and resid 202 through 208 Processing helix chain 'D' and resid 47 through 51 Processing helix chain 'D' and resid 106 through 110 removed outlier: 3.931A pdb=" N THR D 110 " --> pdb=" O SER D 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 24 through 25 removed outlier: 3.652A pdb=" N ASP C 90 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 30 through 33 removed outlier: 6.730A pdb=" N VAL C 53 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TYR C 69 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N TRP C 55 " --> pdb=" O LEU C 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 135 through 138 removed outlier: 3.908A pdb=" N VAL C 153 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN C 158 " --> pdb=" O TYR C 193 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N TYR C 193 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 165 through 170 Processing sheet with id=AA5, first strand: chain 'D' and resid 22 through 25 Processing sheet with id=AA6, first strand: chain 'D' and resid 29 through 31 removed outlier: 6.537A pdb=" N MET D 53 " --> pdb=" O TRP D 69 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TRP D 69 " --> pdb=" O MET D 53 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TRP D 55 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 145 through 149 removed outlier: 4.103A pdb=" N LEU D 166 " --> pdb=" O TYR D 147 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY D 164 " --> pdb=" O LEU D 149 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N TYR D 200 " --> pdb=" O GLY D 169 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU D 199 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU D 195 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N THR D 201 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA D 193 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER D 203 " --> pdb=" O PHE D 191 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 176 through 179 439 hydrogen bonds defined for protein. 1251 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: 1.88 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2020 1.34 - 1.46: 1505 1.46 - 1.58: 2742 1.58 - 1.70: 0 1.70 - 1.81: 55 Bond restraints: 6322 Sorted by residual: bond pdb=" CB PRO C 60 " pdb=" CG PRO C 60 " ideal model delta sigma weight residual 1.492 1.558 -0.066 5.00e-02 4.00e+02 1.76e+00 bond pdb=" N GLU D 61 " pdb=" CA GLU D 61 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.18e+00 bond pdb=" CG PRO D 33 " pdb=" CD PRO D 33 " ideal model delta sigma weight residual 1.503 1.539 -0.036 3.40e-02 8.65e+02 1.11e+00 bond pdb=" C ILE A 463 " pdb=" O ILE A 463 " ideal model delta sigma weight residual 1.237 1.248 -0.011 1.13e-02 7.83e+03 9.60e-01 bond pdb=" CB ILE A 467 " pdb=" CG2 ILE A 467 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.23e-01 ... (remaining 6317 not shown) Histogram of bond angle deviations from ideal: 99.10 - 106.08: 102 106.08 - 113.06: 3477 113.06 - 120.05: 2034 120.05 - 127.03: 2955 127.03 - 134.01: 55 Bond angle restraints: 8623 Sorted by residual: angle pdb=" CA PRO C 60 " pdb=" N PRO C 60 " pdb=" CD PRO C 60 " ideal model delta sigma weight residual 112.00 107.19 4.81 1.40e+00 5.10e-01 1.18e+01 angle pdb=" N PRO C 60 " pdb=" CA PRO C 60 " pdb=" C PRO C 60 " ideal model delta sigma weight residual 110.21 113.94 -3.73 1.64e+00 3.72e-01 5.19e+00 angle pdb=" CG ARG A 365 " pdb=" CD ARG A 365 " pdb=" NE ARG A 365 " ideal model delta sigma weight residual 112.00 116.66 -4.66 2.20e+00 2.07e-01 4.48e+00 angle pdb=" N GLU A 290 " pdb=" CA GLU A 290 " pdb=" C GLU A 290 " ideal model delta sigma weight residual 109.81 114.48 -4.67 2.21e+00 2.05e-01 4.46e+00 angle pdb=" CA PRO D 33 " pdb=" N PRO D 33 " pdb=" CD PRO D 33 " ideal model delta sigma weight residual 112.00 109.24 2.76 1.40e+00 5.10e-01 3.89e+00 ... (remaining 8618 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 3202 17.96 - 35.91: 336 35.91 - 53.87: 128 53.87 - 71.83: 10 71.83 - 89.78: 3 Dihedral angle restraints: 3679 sinusoidal: 1170 harmonic: 2509 Sorted by residual: dihedral pdb=" CB CYS A 367 " pdb=" SG CYS A 367 " pdb=" SG CYS A 553 " pdb=" CB CYS A 553 " ideal model delta sinusoidal sigma weight residual -86.00 -113.49 27.49 1 1.00e+01 1.00e-02 1.08e+01 dihedral pdb=" CA ASN A 141 " pdb=" CB ASN A 141 " pdb=" CG ASN A 141 " pdb=" OD1 ASN A 141 " ideal model delta sinusoidal sigma weight residual 120.00 -169.77 -70.23 2 2.00e+01 2.50e-03 1.06e+01 dihedral pdb=" CA ASP D 80 " pdb=" CB ASP D 80 " pdb=" CG ASP D 80 " pdb=" OD1 ASP D 80 " ideal model delta sinusoidal sigma weight residual -30.00 -84.96 54.96 1 2.00e+01 2.50e-03 1.02e+01 ... (remaining 3676 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 605 0.027 - 0.054: 263 0.054 - 0.081: 89 0.081 - 0.108: 52 0.108 - 0.135: 17 Chirality restraints: 1026 Sorted by residual: chirality pdb=" CA GLU A 290 " pdb=" N GLU A 290 " pdb=" C GLU A 290 " pdb=" CB GLU A 290 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CB ILE A 467 " pdb=" CA ILE A 467 " pdb=" CG1 ILE A 467 " pdb=" CG2 ILE A 467 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA ILE C 95 " pdb=" N ILE C 95 " pdb=" C ILE C 95 " pdb=" CB ILE C 95 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 1023 not shown) Planarity restraints: 1095 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 32 " -0.068 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO D 33 " 0.177 5.00e-02 4.00e+02 pdb=" CA PRO D 33 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO D 33 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 516 " 0.066 5.00e-02 4.00e+02 9.98e-02 1.59e+01 pdb=" N PRO A 517 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO A 517 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 517 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 59 " 0.059 5.00e-02 4.00e+02 8.78e-02 1.23e+01 pdb=" N PRO C 60 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO C 60 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 60 " 0.049 5.00e-02 4.00e+02 ... (remaining 1092 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 5 2.27 - 2.93: 2691 2.93 - 3.58: 8950 3.58 - 4.24: 12970 4.24 - 4.90: 22833 Nonbonded interactions: 47449 Sorted by model distance: nonbonded pdb=" SG CYS A 326 " pdb="CO CO A 602 " model vdw 1.612 2.580 nonbonded pdb=" OD2 ASP A 39 " pdb="CO CO A 601 " model vdw 2.026 2.220 nonbonded pdb=" NE2 HIS A 507 " pdb="CO CO A 602 " model vdw 2.130 2.300 nonbonded pdb=" NE2 HIS A 43 " pdb="CO CO A 601 " model vdw 2.145 2.300 nonbonded pdb=" OG SER C 34 " pdb=" OD2 ASP C 37 " model vdw 2.239 2.440 ... (remaining 47444 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.160 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 22.440 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 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 : 0.003 0.066 6322 Z= 0.176 Angle : 0.534 6.857 8623 Z= 0.285 Chirality : 0.040 0.135 1026 Planarity : 0.007 0.102 1095 Dihedral : 16.820 89.785 2066 Min Nonbonded Distance : 1.612 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.54 % Favored : 97.35 % Rotamer: Outliers : 3.54 % Allowed : 35.40 % Favored : 61.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.02 (0.30), residues: 867 helix: 2.75 (0.25), residues: 402 sheet: 1.13 (0.41), residues: 198 loop : -0.77 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 69 HIS 0.003 0.001 HIS A 32 PHE 0.009 0.001 PHE C 107 TYR 0.008 0.001 TYR A 64 ARG 0.007 0.001 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 180 time to evaluate : 0.743 Fit side-chains revert: symmetry clash REVERT: A 129 LEU cc_start: 0.8973 (tp) cc_final: 0.8089 (tp) REVERT: D 62 GLN cc_start: 0.8254 (tp40) cc_final: 0.7551 (mp10) outliers start: 20 outliers final: 10 residues processed: 196 average time/residue: 1.0280 time to fit residues: 212.2641 Evaluate side-chains 136 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 103 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 20.0000 chunk 43 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 78 optimal weight: 50.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS A 118 HIS A 182 GLN C 48 ASN D 22 GLN D 24 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6322 Z= 0.335 Angle : 0.616 7.428 8623 Z= 0.324 Chirality : 0.042 0.151 1026 Planarity : 0.005 0.066 1095 Dihedral : 4.914 58.992 942 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.11 % Favored : 96.77 % Rotamer: Outliers : 8.67 % Allowed : 31.50 % Favored : 59.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.33 (0.29), residues: 867 helix: 2.93 (0.25), residues: 409 sheet: 1.16 (0.38), residues: 207 loop : -0.53 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 37 HIS 0.010 0.002 HIS A 118 PHE 0.015 0.001 PHE C 107 TYR 0.013 0.001 TYR C 160 ARG 0.008 0.001 ARG D 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 116 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8331 (t0) cc_final: 0.8026 (t0) REVERT: C 48 ASN cc_start: 0.8582 (t0) cc_final: 0.8346 (t0) outliers start: 49 outliers final: 17 residues processed: 152 average time/residue: 1.0136 time to fit residues: 162.7240 Evaluate side-chains 123 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 106 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 211 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 64 optimal weight: 20.0000 chunk 53 optimal weight: 0.2980 chunk 21 optimal weight: 0.3980 chunk 78 optimal weight: 50.0000 chunk 84 optimal weight: 50.0000 chunk 69 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 26 optimal weight: 0.0270 chunk 62 optimal weight: 6.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN D 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6322 Z= 0.183 Angle : 0.583 8.008 8623 Z= 0.292 Chirality : 0.041 0.151 1026 Planarity : 0.004 0.058 1095 Dihedral : 4.231 58.773 931 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.42 % Favored : 97.46 % Rotamer: Outliers : 6.73 % Allowed : 33.45 % Favored : 59.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.51 (0.30), residues: 867 helix: 3.13 (0.25), residues: 408 sheet: 1.28 (0.38), residues: 203 loop : -0.53 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 69 HIS 0.010 0.001 HIS A 118 PHE 0.011 0.001 PHE C 30 TYR 0.008 0.001 TYR A 538 ARG 0.007 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 124 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8043 (t0) cc_final: 0.7678 (t0) REVERT: A 324 PHE cc_start: 0.8627 (OUTLIER) cc_final: 0.8071 (t80) REVERT: A 364 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.7463 (ttp-110) REVERT: C 48 ASN cc_start: 0.8568 (t0) cc_final: 0.8324 (t0) REVERT: D 61 GLU cc_start: 0.7413 (pp20) cc_final: 0.6995 (pp20) REVERT: D 62 GLN cc_start: 0.8438 (tp40) cc_final: 0.7900 (mp10) outliers start: 38 outliers final: 15 residues processed: 145 average time/residue: 1.1110 time to fit residues: 169.8023 Evaluate side-chains 132 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 107 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 83 optimal weight: 30.0000 chunk 41 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6322 Z= 0.334 Angle : 0.614 8.161 8623 Z= 0.317 Chirality : 0.042 0.148 1026 Planarity : 0.004 0.055 1095 Dihedral : 3.850 44.112 929 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.23 % Favored : 96.66 % Rotamer: Outliers : 7.61 % Allowed : 32.57 % Favored : 59.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.48 (0.30), residues: 867 helix: 3.08 (0.25), residues: 407 sheet: 1.26 (0.38), residues: 203 loop : -0.47 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 69 HIS 0.011 0.002 HIS A 118 PHE 0.008 0.001 PHE C 107 TYR 0.014 0.001 TYR C 160 ARG 0.006 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 109 time to evaluate : 0.886 Fit side-chains revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8343 (t0) cc_final: 0.7991 (t0) REVERT: A 324 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8320 (t80) REVERT: A 364 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.7599 (ttp-110) REVERT: C 48 ASN cc_start: 0.8664 (t0) cc_final: 0.8464 (t0) REVERT: C 107 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.8186 (p90) outliers start: 43 outliers final: 23 residues processed: 139 average time/residue: 1.1114 time to fit residues: 162.7129 Evaluate side-chains 129 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 103 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 211 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6322 Z= 0.313 Angle : 0.626 9.667 8623 Z= 0.320 Chirality : 0.042 0.161 1026 Planarity : 0.004 0.052 1095 Dihedral : 3.879 44.475 929 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.23 % Favored : 96.66 % Rotamer: Outliers : 7.08 % Allowed : 33.10 % Favored : 59.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.43 (0.29), residues: 867 helix: 3.03 (0.25), residues: 407 sheet: 1.18 (0.37), residues: 210 loop : -0.48 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 69 HIS 0.012 0.002 HIS A 118 PHE 0.009 0.001 PHE A 324 TYR 0.013 0.001 TYR C 160 ARG 0.005 0.000 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 109 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: A 165 GLU cc_start: 0.7042 (mm-30) cc_final: 0.6734 (mm-30) REVERT: A 166 ASP cc_start: 0.8232 (t0) cc_final: 0.7904 (t0) REVERT: A 324 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.8347 (t80) REVERT: A 364 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.7520 (ttp-110) REVERT: C 48 ASN cc_start: 0.8663 (t0) cc_final: 0.8455 (t0) REVERT: D 62 GLN cc_start: 0.8571 (tp40) cc_final: 0.8224 (mm-40) REVERT: D 119 ARG cc_start: 0.8396 (tpt-90) cc_final: 0.8193 (tpt90) outliers start: 40 outliers final: 20 residues processed: 137 average time/residue: 1.0987 time to fit residues: 158.6863 Evaluate side-chains 126 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 211 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 0.0030 chunk 74 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 83 optimal weight: 40.0000 chunk 69 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 0.0270 chunk 43 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 overall best weight: 0.9650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6322 Z= 0.193 Angle : 0.624 10.549 8623 Z= 0.308 Chirality : 0.042 0.163 1026 Planarity : 0.004 0.052 1095 Dihedral : 3.779 46.149 928 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.00 % Favored : 96.89 % Rotamer: Outliers : 6.55 % Allowed : 35.04 % Favored : 58.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.53 (0.30), residues: 867 helix: 3.13 (0.25), residues: 402 sheet: 1.35 (0.37), residues: 203 loop : -0.46 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 69 HIS 0.012 0.002 HIS A 118 PHE 0.008 0.001 PHE A 324 TYR 0.007 0.001 TYR A 64 ARG 0.009 0.000 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 114 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: A 165 GLU cc_start: 0.6942 (mm-30) cc_final: 0.6705 (mm-30) REVERT: A 166 ASP cc_start: 0.7965 (t0) cc_final: 0.7546 (t0) REVERT: A 324 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.8424 (t80) REVERT: A 364 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.7317 (ttp-110) REVERT: C 48 ASN cc_start: 0.8663 (t0) cc_final: 0.8463 (t0) REVERT: D 119 ARG cc_start: 0.8357 (tpt-90) cc_final: 0.8089 (tpt90) outliers start: 37 outliers final: 17 residues processed: 140 average time/residue: 1.0732 time to fit residues: 158.4196 Evaluate side-chains 122 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 107 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 60 optimal weight: 30.0000 chunk 70 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 82 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6322 Z= 0.320 Angle : 0.678 12.015 8623 Z= 0.339 Chirality : 0.043 0.195 1026 Planarity : 0.004 0.050 1095 Dihedral : 3.829 45.753 928 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.11 % Favored : 96.77 % Rotamer: Outliers : 6.19 % Allowed : 37.17 % Favored : 56.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.43 (0.29), residues: 867 helix: 3.05 (0.25), residues: 401 sheet: 1.20 (0.36), residues: 210 loop : -0.44 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 299 HIS 0.012 0.002 HIS A 118 PHE 0.015 0.001 PHE C 30 TYR 0.012 0.001 TYR C 160 ARG 0.006 0.000 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 104 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8247 (t0) cc_final: 0.7861 (t0) REVERT: A 324 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.8426 (t80) REVERT: A 364 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.7470 (ttp-110) outliers start: 35 outliers final: 17 residues processed: 128 average time/residue: 1.0812 time to fit residues: 145.8401 Evaluate side-chains 121 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 79 optimal weight: 50.0000 chunk 72 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6322 Z= 0.212 Angle : 0.672 12.432 8623 Z= 0.328 Chirality : 0.042 0.213 1026 Planarity : 0.004 0.051 1095 Dihedral : 3.787 45.271 928 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.88 % Favored : 97.00 % Rotamer: Outliers : 4.78 % Allowed : 39.12 % Favored : 56.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.49 (0.29), residues: 867 helix: 3.05 (0.26), residues: 402 sheet: 1.29 (0.37), residues: 202 loop : -0.35 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 69 HIS 0.013 0.002 HIS A 118 PHE 0.007 0.001 PHE A 295 TYR 0.008 0.001 TYR A 64 ARG 0.012 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 112 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: A 166 ASP cc_start: 0.7926 (t0) cc_final: 0.7496 (t0) REVERT: A 364 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.7322 (ttp-110) REVERT: D 51 TYR cc_start: 0.8382 (m-80) cc_final: 0.7937 (m-80) outliers start: 27 outliers final: 17 residues processed: 132 average time/residue: 1.0213 time to fit residues: 142.2961 Evaluate side-chains 124 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 106 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain D residue 57 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 0.9980 chunk 46 optimal weight: 9.9990 chunk 33 optimal weight: 0.0270 chunk 60 optimal weight: 30.0000 chunk 23 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 chunk 49 optimal weight: 3.9990 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 141 ASN ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6322 Z= 0.209 Angle : 0.688 12.999 8623 Z= 0.334 Chirality : 0.043 0.242 1026 Planarity : 0.004 0.050 1095 Dihedral : 3.749 44.742 928 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.00 % Favored : 96.89 % Rotamer: Outliers : 3.89 % Allowed : 40.00 % Favored : 56.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.52 (0.29), residues: 867 helix: 3.07 (0.26), residues: 401 sheet: 1.35 (0.37), residues: 202 loop : -0.36 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 69 HIS 0.005 0.001 HIS A 118 PHE 0.014 0.001 PHE C 30 TYR 0.006 0.001 TYR C 111 ARG 0.008 0.000 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 114 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 364 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.7294 (ttp-110) REVERT: D 61 GLU cc_start: 0.7916 (pp20) cc_final: 0.7494 (pp20) REVERT: D 119 ARG cc_start: 0.8350 (tpp80) cc_final: 0.7697 (tpt-90) outliers start: 22 outliers final: 14 residues processed: 130 average time/residue: 1.0469 time to fit residues: 143.5485 Evaluate side-chains 116 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain D residue 57 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 85 optimal weight: 30.0000 chunk 78 optimal weight: 50.0000 chunk 68 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 144 ASN ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6322 Z= 0.281 Angle : 0.748 13.061 8623 Z= 0.359 Chirality : 0.044 0.273 1026 Planarity : 0.004 0.050 1095 Dihedral : 3.904 49.100 928 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.11 % Favored : 96.77 % Rotamer: Outliers : 4.42 % Allowed : 39.65 % Favored : 55.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.46 (0.29), residues: 867 helix: 2.99 (0.26), residues: 403 sheet: 1.35 (0.37), residues: 202 loop : -0.38 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 211 HIS 0.013 0.002 HIS A 118 PHE 0.008 0.001 PHE A 324 TYR 0.012 0.001 TYR A 501 ARG 0.007 0.000 ARG C 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 101 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: A 324 PHE cc_start: 0.8859 (OUTLIER) cc_final: 0.8444 (t80) REVERT: A 364 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.7440 (ttp-110) outliers start: 25 outliers final: 15 residues processed: 118 average time/residue: 1.0743 time to fit residues: 133.6081 Evaluate side-chains 115 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 0.0470 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 59 optimal weight: 30.0000 chunk 3 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.079423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.060512 restraints weight = 18035.278| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 3.65 r_work: 0.2687 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6322 Z= 0.211 Angle : 0.745 12.703 8623 Z= 0.352 Chirality : 0.044 0.270 1026 Planarity : 0.004 0.059 1095 Dihedral : 3.876 47.846 928 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.00 % Favored : 96.89 % Rotamer: Outliers : 4.07 % Allowed : 40.18 % Favored : 55.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.45 (0.30), residues: 867 helix: 2.98 (0.26), residues: 401 sheet: 1.37 (0.37), residues: 202 loop : -0.39 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 211 HIS 0.006 0.001 HIS A 118 PHE 0.016 0.001 PHE C 30 TYR 0.012 0.001 TYR A 501 ARG 0.015 0.001 ARG C 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2814.06 seconds wall clock time: 50 minutes 36.08 seconds (3036.08 seconds total)