Starting phenix.real_space_refine on Tue Mar 11 15:09:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dl8_27499/03_2025/8dl8_27499.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dl8_27499/03_2025/8dl8_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/cci-nas-00/data/ceres_data/8dl8_27499/03_2025/8dl8_27499.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dl8_27499/03_2025/8dl8_27499.map" model { file = "/net/cci-nas-00/data/ceres_data/8dl8_27499/03_2025/8dl8_27499.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dl8_27499/03_2025/8dl8_27499.cif" } 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. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 4.00, per 1000 atoms: 0.64 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 910.8 milliseconds 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: 0.71 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: 2.11 Time building geometry restraints manager: 1.80 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: 0.00 - 1.37: 8413 1.37 - 2.74: 160 2.74 - 4.11: 32 4.11 - 5.49: 14 5.49 - 6.86: 4 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 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.570 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:13.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.700 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.658 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: 0.9663 time to fit residues: 199.9581 Evaluate side-chains 136 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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: 9.9990 chunk 65 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 78 optimal weight: 50.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 26 GLN C 48 ASN D 22 GLN D 24 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.076930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.057488 restraints weight = 18066.104| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 3.60 r_work: 0.2636 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6322 Z= 0.285 Angle : 0.608 7.580 8623 Z= 0.317 Chirality : 0.042 0.137 1026 Planarity : 0.005 0.067 1095 Dihedral : 5.185 59.650 942 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.88 % Favored : 97.00 % Rotamer: Outliers : 8.50 % Allowed : 31.86 % Favored : 59.65 % 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: 2.39 (0.30), residues: 867 helix: 2.99 (0.25), residues: 409 sheet: 1.15 (0.38), residues: 206 loop : -0.48 (0.39), residues: 252 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 0.013 0.001 PHE C 107 TYR 0.012 0.001 TYR A 538 ARG 0.008 0.001 ARG C 38 *********************** 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 174 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 126 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 SER cc_start: 0.9638 (m) cc_final: 0.9390 (p) REVERT: A 119 GLU cc_start: 0.9148 (tp30) cc_final: 0.8791 (tp30) REVERT: A 166 ASP cc_start: 0.8826 (t0) cc_final: 0.7794 (t0) REVERT: A 219 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8571 (mt-10) REVERT: A 228 GLN cc_start: 0.9366 (OUTLIER) cc_final: 0.9143 (mt0) REVERT: A 324 PHE cc_start: 0.9278 (OUTLIER) cc_final: 0.8093 (t80) REVERT: A 529 SER cc_start: 0.9567 (OUTLIER) cc_final: 0.9351 (p) REVERT: C 38 ARG cc_start: 0.9388 (ptm160) cc_final: 0.9150 (mtp-110) REVERT: C 48 ASN cc_start: 0.9533 (t0) cc_final: 0.9299 (t0) REVERT: C 62 GLN cc_start: 0.8393 (mp10) cc_final: 0.8138 (mp10) REVERT: C 69 TYR cc_start: 0.9469 (p90) cc_final: 0.9172 (p90) REVERT: C 70 SER cc_start: 0.9712 (OUTLIER) cc_final: 0.9051 (p) REVERT: C 101 GLU cc_start: 0.9086 (pm20) cc_final: 0.8829 (pm20) REVERT: D 61 GLU cc_start: 0.8504 (pp20) cc_final: 0.7746 (pp20) REVERT: D 62 GLN cc_start: 0.9270 (tp40) cc_final: 0.8212 (mp10) outliers start: 48 outliers final: 17 residues processed: 160 average time/residue: 0.9663 time to fit residues: 163.4759 Evaluate side-chains 132 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 338 SER 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 511 VAL Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 70 SER 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 136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 41 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 61 optimal weight: 20.0000 chunk 77 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 64 optimal weight: 50.0000 chunk 33 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 overall best weight: 1.6982 ------------------------------------------------------------------------------- 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 D 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.077564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.058385 restraints weight = 18230.077| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 3.59 r_work: 0.2624 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6322 Z= 0.233 Angle : 0.580 7.600 8623 Z= 0.296 Chirality : 0.041 0.149 1026 Planarity : 0.004 0.058 1095 Dihedral : 4.634 59.414 932 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.65 % Favored : 97.23 % Rotamer: Outliers : 6.90 % Allowed : 31.86 % Favored : 61.24 % 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: 2.55 (0.30), residues: 867 helix: 3.13 (0.25), residues: 407 sheet: 1.25 (0.38), residues: 207 loop : -0.44 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 69 HIS 0.010 0.002 HIS A 118 PHE 0.012 0.001 PHE C 30 TYR 0.009 0.001 TYR C 160 ARG 0.004 0.001 ARG D 32 *********************** 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 158 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 119 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 SER cc_start: 0.9587 (m) cc_final: 0.9334 (p) REVERT: A 119 GLU cc_start: 0.9133 (tp30) cc_final: 0.8818 (tp30) REVERT: A 166 ASP cc_start: 0.8742 (t0) cc_final: 0.7675 (t0) REVERT: A 219 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8510 (mt-10) REVERT: A 228 GLN cc_start: 0.9370 (OUTLIER) cc_final: 0.9120 (mt0) REVERT: A 324 PHE cc_start: 0.9288 (OUTLIER) cc_final: 0.8380 (t80) REVERT: A 364 ARG cc_start: 0.9284 (OUTLIER) cc_final: 0.7509 (ttp-110) REVERT: C 34 SER cc_start: 0.8604 (OUTLIER) cc_final: 0.8338 (p) REVERT: C 39 VAL cc_start: 0.9595 (t) cc_final: 0.9328 (m) REVERT: C 62 GLN cc_start: 0.8328 (mp10) cc_final: 0.8081 (mp10) REVERT: C 69 TYR cc_start: 0.9457 (p90) cc_final: 0.9217 (p90) REVERT: C 70 SER cc_start: 0.9711 (OUTLIER) cc_final: 0.9053 (p) REVERT: C 101 GLU cc_start: 0.9151 (pm20) cc_final: 0.8814 (pm20) REVERT: D 29 GLU cc_start: 0.9345 (mm-30) cc_final: 0.8275 (mp0) outliers start: 39 outliers final: 13 residues processed: 144 average time/residue: 1.0985 time to fit residues: 166.4335 Evaluate side-chains 126 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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 120 LEU Chi-restraints excluded: chain A residue 228 GLN 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 C residue 25 THR Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 83 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 Chi-restraints excluded: chain D residue 61 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 0.0030 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 57 optimal weight: 20.0000 chunk 45 optimal weight: 6.9990 chunk 41 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.077796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.059397 restraints weight = 18289.777| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 3.64 r_work: 0.2662 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2422 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= 0.178 Angle : 0.575 8.567 8623 Z= 0.289 Chirality : 0.041 0.149 1026 Planarity : 0.004 0.056 1095 Dihedral : 4.083 50.648 930 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.11 % Favored : 96.77 % Rotamer: Outliers : 6.73 % Allowed : 31.68 % Favored : 61.59 % 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: 2.64 (0.30), residues: 867 helix: 3.15 (0.25), residues: 408 sheet: 1.41 (0.38), residues: 205 loop : -0.38 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 69 HIS 0.011 0.001 HIS A 118 PHE 0.008 0.001 PHE A 295 TYR 0.007 0.001 TYR A 538 ARG 0.007 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 160 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 SER cc_start: 0.9585 (m) cc_final: 0.9358 (p) REVERT: A 119 GLU cc_start: 0.9129 (tp30) cc_final: 0.8715 (tm-30) REVERT: A 120 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.9046 (mm) REVERT: A 127 TRP cc_start: 0.7930 (t60) cc_final: 0.7426 (t-100) REVERT: A 166 ASP cc_start: 0.8656 (t0) cc_final: 0.7527 (t0) REVERT: A 219 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8527 (mt-10) REVERT: A 228 GLN cc_start: 0.9354 (OUTLIER) cc_final: 0.9145 (mt0) REVERT: A 324 PHE cc_start: 0.9293 (OUTLIER) cc_final: 0.8555 (t80) REVERT: A 364 ARG cc_start: 0.9222 (OUTLIER) cc_final: 0.7350 (ttp-110) REVERT: A 473 ASP cc_start: 0.9660 (t0) cc_final: 0.9430 (t0) REVERT: C 34 SER cc_start: 0.8617 (OUTLIER) cc_final: 0.8327 (p) REVERT: C 39 VAL cc_start: 0.9630 (t) cc_final: 0.9361 (m) REVERT: C 62 GLN cc_start: 0.8459 (mp10) cc_final: 0.8175 (mp10) REVERT: C 70 SER cc_start: 0.9687 (OUTLIER) cc_final: 0.9131 (p) REVERT: C 101 GLU cc_start: 0.9201 (pm20) cc_final: 0.8801 (pm20) REVERT: C 125 GLU cc_start: 0.7814 (tp30) cc_final: 0.7385 (tm-30) REVERT: D 29 GLU cc_start: 0.9322 (mm-30) cc_final: 0.8236 (mp0) REVERT: D 61 GLU cc_start: 0.8604 (pp20) cc_final: 0.8154 (pp20) REVERT: D 62 GLN cc_start: 0.9270 (tp40) cc_final: 0.8307 (mp10) outliers start: 38 outliers final: 14 residues processed: 148 average time/residue: 1.0125 time to fit residues: 158.4949 Evaluate side-chains 131 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 120 LEU Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 228 GLN 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 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 83 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 2 optimal weight: 0.7980 chunk 44 optimal weight: 0.1980 chunk 53 optimal weight: 2.9990 chunk 6 optimal weight: 0.0670 chunk 34 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 63 optimal weight: 40.0000 chunk 52 optimal weight: 3.9990 chunk 60 optimal weight: 40.0000 chunk 45 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 overall best weight: 1.0120 ------------------------------------------------------------------------------- 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 A 182 GLN C 48 ASN C 109 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.078112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.059414 restraints weight = 18395.291| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 3.67 r_work: 0.2663 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2567 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= 0.185 Angle : 0.587 9.558 8623 Z= 0.289 Chirality : 0.041 0.150 1026 Planarity : 0.004 0.054 1095 Dihedral : 3.974 46.106 930 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.88 % Favored : 97.00 % Rotamer: Outliers : 5.84 % Allowed : 33.10 % 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: 2.64 (0.30), residues: 867 helix: 3.11 (0.25), residues: 408 sheet: 1.48 (0.38), residues: 201 loop : -0.35 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 69 HIS 0.011 0.001 HIS A 118 PHE 0.013 0.001 PHE C 30 TYR 0.007 0.001 TYR A 64 ARG 0.006 0.001 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 161 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 TRP cc_start: 0.9113 (t-100) cc_final: 0.8864 (t-100) REVERT: A 102 SER cc_start: 0.9567 (m) cc_final: 0.9329 (p) REVERT: A 119 GLU cc_start: 0.9128 (tp30) cc_final: 0.8700 (tm-30) REVERT: A 120 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8979 (mm) REVERT: A 127 TRP cc_start: 0.7918 (t60) cc_final: 0.7417 (t-100) REVERT: A 166 ASP cc_start: 0.8522 (t0) cc_final: 0.7856 (t0) REVERT: A 228 GLN cc_start: 0.9339 (OUTLIER) cc_final: 0.9089 (mt0) REVERT: A 324 PHE cc_start: 0.9303 (OUTLIER) cc_final: 0.8715 (t80) REVERT: A 364 ARG cc_start: 0.9173 (OUTLIER) cc_final: 0.7295 (ttp-110) REVERT: A 473 ASP cc_start: 0.9644 (t0) cc_final: 0.9403 (t0) REVERT: C 38 ARG cc_start: 0.9457 (ptm160) cc_final: 0.9245 (mtp-110) REVERT: C 39 VAL cc_start: 0.9621 (t) cc_final: 0.9318 (m) REVERT: C 62 GLN cc_start: 0.8491 (mp10) cc_final: 0.8215 (mp10) REVERT: C 69 TYR cc_start: 0.9409 (p90) cc_final: 0.9167 (p90) REVERT: C 70 SER cc_start: 0.9673 (OUTLIER) cc_final: 0.9065 (p) REVERT: C 101 GLU cc_start: 0.9199 (pm20) cc_final: 0.8784 (pm20) REVERT: C 125 GLU cc_start: 0.7835 (tp30) cc_final: 0.7394 (tm-30) REVERT: D 29 GLU cc_start: 0.9256 (mm-30) cc_final: 0.8139 (mp0) outliers start: 33 outliers final: 13 residues processed: 152 average time/residue: 1.0035 time to fit residues: 161.1673 Evaluate side-chains 132 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 228 GLN 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 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 83 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 61 GLU Chi-restraints excluded: chain D residue 107 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 57 optimal weight: 20.0000 chunk 59 optimal weight: 40.0000 chunk 66 optimal weight: 8.9990 chunk 78 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 82 optimal weight: 30.0000 chunk 55 optimal weight: 30.0000 chunk 5 optimal weight: 0.7980 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 C 109 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.077192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.057749 restraints weight = 18168.210| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 3.65 r_work: 0.2648 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6322 Z= 0.241 Angle : 0.623 9.447 8623 Z= 0.306 Chirality : 0.042 0.149 1026 Planarity : 0.004 0.054 1095 Dihedral : 3.733 45.596 929 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.34 % Favored : 96.54 % Rotamer: Outliers : 5.49 % Allowed : 34.34 % Favored : 60.18 % 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: 2.63 (0.29), residues: 867 helix: 3.09 (0.25), residues: 407 sheet: 1.47 (0.38), residues: 201 loop : -0.31 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 211 HIS 0.011 0.002 HIS A 118 PHE 0.007 0.001 PHE C 107 TYR 0.009 0.001 TYR C 160 ARG 0.003 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 149 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: A 17 LEU cc_start: 0.8760 (pt) cc_final: 0.8353 (tm) REVERT: A 102 SER cc_start: 0.9594 (m) cc_final: 0.9385 (p) REVERT: A 119 GLU cc_start: 0.9157 (tp30) cc_final: 0.8723 (tm-30) REVERT: A 120 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8975 (mm) REVERT: A 127 TRP cc_start: 0.7999 (t60) cc_final: 0.7508 (t-100) REVERT: A 165 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7038 (mm-30) REVERT: A 166 ASP cc_start: 0.8676 (t0) cc_final: 0.7516 (t0) REVERT: A 196 MET cc_start: 0.9341 (tpp) cc_final: 0.9100 (tpt) REVERT: A 324 PHE cc_start: 0.9334 (OUTLIER) cc_final: 0.8721 (t80) REVERT: A 364 ARG cc_start: 0.9280 (OUTLIER) cc_final: 0.7432 (ttp-110) REVERT: A 473 ASP cc_start: 0.9654 (t0) cc_final: 0.9422 (t0) REVERT: C 39 VAL cc_start: 0.9594 (t) cc_final: 0.9147 (m) REVERT: C 62 GLN cc_start: 0.8587 (mp10) cc_final: 0.8280 (mp10) REVERT: C 69 TYR cc_start: 0.9519 (p90) cc_final: 0.9248 (p90) REVERT: C 70 SER cc_start: 0.9723 (OUTLIER) cc_final: 0.9179 (p) REVERT: C 101 GLU cc_start: 0.9197 (pm20) cc_final: 0.8868 (pm20) REVERT: C 125 GLU cc_start: 0.7824 (tp30) cc_final: 0.7401 (tm-30) REVERT: D 24 GLN cc_start: 0.9328 (mm110) cc_final: 0.9117 (mm-40) REVERT: D 29 GLU cc_start: 0.9280 (mm-30) cc_final: 0.8183 (mp0) REVERT: D 42 LYS cc_start: 0.9326 (ttmm) cc_final: 0.8954 (ttpp) REVERT: D 62 GLN cc_start: 0.9243 (tp40) cc_final: 0.8364 (mm-40) REVERT: D 118 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.8883 (tptp) REVERT: D 119 ARG cc_start: 0.8986 (tpt-90) cc_final: 0.8712 (tpt90) outliers start: 31 outliers final: 15 residues processed: 141 average time/residue: 1.0897 time to fit residues: 161.7482 Evaluate side-chains 133 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU 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 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 512 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 83 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 Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 118 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 41 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 30 optimal weight: 0.2980 chunk 8 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 182 GLN C 109 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.078988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.059447 restraints weight = 18149.421| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 3.70 r_work: 0.2665 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2845 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= 0.178 Angle : 0.627 10.361 8623 Z= 0.301 Chirality : 0.041 0.157 1026 Planarity : 0.004 0.054 1095 Dihedral : 3.674 44.902 929 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.00 % Favored : 96.89 % Rotamer: Outliers : 5.66 % Allowed : 34.34 % Favored : 60.00 % 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: 2.60 (0.29), residues: 867 helix: 3.05 (0.25), residues: 408 sheet: 1.44 (0.37), residues: 207 loop : -0.35 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 211 HIS 0.011 0.001 HIS A 118 PHE 0.008 0.001 PHE A 295 TYR 0.007 0.001 TYR A 64 ARG 0.007 0.001 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 158 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LEU cc_start: 0.8778 (pt) cc_final: 0.8395 (tm) REVERT: A 102 SER cc_start: 0.9566 (m) cc_final: 0.9322 (p) REVERT: A 119 GLU cc_start: 0.9136 (tp30) cc_final: 0.8717 (tm-30) REVERT: A 120 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8932 (mm) REVERT: A 127 TRP cc_start: 0.7952 (t60) cc_final: 0.7456 (t-100) REVERT: A 166 ASP cc_start: 0.8474 (t0) cc_final: 0.7806 (t0) REVERT: A 196 MET cc_start: 0.9309 (tpp) cc_final: 0.9099 (tpt) REVERT: A 324 PHE cc_start: 0.9303 (OUTLIER) cc_final: 0.8800 (t80) REVERT: A 364 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.7231 (ttp-110) REVERT: A 473 ASP cc_start: 0.9645 (t0) cc_final: 0.9411 (t0) REVERT: C 39 VAL cc_start: 0.9530 (t) cc_final: 0.9218 (m) REVERT: C 62 GLN cc_start: 0.8551 (mp10) cc_final: 0.8242 (mp10) REVERT: C 69 TYR cc_start: 0.9429 (p90) cc_final: 0.9187 (p90) REVERT: C 70 SER cc_start: 0.9698 (OUTLIER) cc_final: 0.9135 (p) REVERT: C 101 GLU cc_start: 0.9211 (pm20) cc_final: 0.8815 (pm20) REVERT: D 24 GLN cc_start: 0.9327 (mm110) cc_final: 0.9113 (mm-40) REVERT: D 29 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8142 (mp0) REVERT: D 31 VAL cc_start: 0.9532 (t) cc_final: 0.9275 (m) REVERT: D 42 LYS cc_start: 0.9235 (ttmm) cc_final: 0.8874 (ttpp) REVERT: D 61 GLU cc_start: 0.8493 (pp20) cc_final: 0.8075 (pp20) REVERT: D 62 GLN cc_start: 0.9104 (tp40) cc_final: 0.8132 (mp10) REVERT: D 118 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8851 (tptp) outliers start: 32 outliers final: 17 residues processed: 148 average time/residue: 0.9972 time to fit residues: 156.0108 Evaluate side-chains 139 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 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 482 GLU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 83 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 Chi-restraints excluded: chain D residue 118 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 41 optimal weight: 0.6980 chunk 80 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 79 optimal weight: 50.0000 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 44 optimal weight: 0.0050 chunk 74 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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 C 48 ASN C 109 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.079583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.061030 restraints weight = 18059.308| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 3.68 r_work: 0.2699 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6322 Z= 0.169 Angle : 0.634 11.072 8623 Z= 0.301 Chirality : 0.042 0.210 1026 Planarity : 0.004 0.054 1095 Dihedral : 3.615 43.992 929 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.77 % Favored : 97.12 % Rotamer: Outliers : 5.13 % Allowed : 35.22 % Favored : 59.65 % 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: 2.61 (0.29), residues: 867 helix: 3.03 (0.25), residues: 409 sheet: 1.49 (0.37), residues: 205 loop : -0.34 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 211 HIS 0.011 0.001 HIS A 118 PHE 0.014 0.001 PHE C 30 TYR 0.008 0.001 TYR A 20 ARG 0.006 0.000 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 160 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LEU cc_start: 0.8716 (pt) cc_final: 0.8342 (tm) REVERT: A 102 SER cc_start: 0.9573 (m) cc_final: 0.9328 (p) REVERT: A 119 GLU cc_start: 0.9126 (tp30) cc_final: 0.8784 (tm-30) REVERT: A 120 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8957 (mm) REVERT: A 123 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8357 (tmm) REVERT: A 127 TRP cc_start: 0.7891 (t60) cc_final: 0.7378 (t-100) REVERT: A 165 GLU cc_start: 0.8951 (mt-10) cc_final: 0.8556 (mt-10) REVERT: A 166 ASP cc_start: 0.8369 (t0) cc_final: 0.7838 (t0) REVERT: A 324 PHE cc_start: 0.9314 (OUTLIER) cc_final: 0.8812 (t80) REVERT: A 364 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.7219 (ttp-110) REVERT: A 467 ILE cc_start: 0.7090 (OUTLIER) cc_final: 0.6814 (tt) REVERT: A 473 ASP cc_start: 0.9640 (t0) cc_final: 0.9381 (t0) REVERT: C 38 ARG cc_start: 0.9486 (ptm160) cc_final: 0.9273 (mtp-110) REVERT: C 39 VAL cc_start: 0.9557 (t) cc_final: 0.9236 (m) REVERT: C 62 GLN cc_start: 0.8554 (mp10) cc_final: 0.8254 (mp10) REVERT: C 69 TYR cc_start: 0.9418 (p90) cc_final: 0.9145 (p90) REVERT: C 70 SER cc_start: 0.9684 (OUTLIER) cc_final: 0.9082 (p) REVERT: C 101 GLU cc_start: 0.9241 (pm20) cc_final: 0.8877 (pm20) REVERT: C 107 PHE cc_start: 0.8964 (p90) cc_final: 0.8749 (p90) REVERT: D 24 GLN cc_start: 0.9362 (mm110) cc_final: 0.9142 (mm-40) REVERT: D 29 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8175 (mp0) REVERT: D 31 VAL cc_start: 0.9550 (t) cc_final: 0.9332 (m) REVERT: D 42 LYS cc_start: 0.9223 (ttmm) cc_final: 0.8864 (ttpp) REVERT: D 118 LYS cc_start: 0.8983 (tppt) cc_final: 0.8722 (tptp) outliers start: 29 outliers final: 13 residues processed: 152 average time/residue: 1.0339 time to fit residues: 165.9025 Evaluate side-chains 137 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 123 MET Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 364 ARG 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 513 LEU Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 83 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 61 GLU Chi-restraints excluded: chain D residue 107 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 42 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 13 optimal weight: 0.2980 chunk 46 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 6 optimal weight: 0.0570 chunk 84 optimal weight: 0.0010 chunk 10 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 overall best weight: 0.3904 ------------------------------------------------------------------------------- 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 C 109 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.081353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.062253 restraints weight = 18184.401| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 3.76 r_work: 0.2745 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6322 Z= 0.180 Angle : 0.674 13.191 8623 Z= 0.315 Chirality : 0.042 0.216 1026 Planarity : 0.004 0.053 1095 Dihedral : 3.695 48.719 929 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.88 % Favored : 97.00 % Rotamer: Outliers : 4.25 % Allowed : 37.17 % Favored : 58.58 % 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: 2.61 (0.29), residues: 867 helix: 2.97 (0.25), residues: 409 sheet: 1.62 (0.38), residues: 199 loop : -0.28 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 211 HIS 0.012 0.001 HIS A 118 PHE 0.008 0.001 PHE A 295 TYR 0.016 0.001 TYR D 51 ARG 0.005 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 154 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.763 Fit side-chains revert: symmetry clash REVERT: A 17 LEU cc_start: 0.8664 (pt) cc_final: 0.8291 (tm) REVERT: A 102 SER cc_start: 0.9572 (m) cc_final: 0.9325 (p) REVERT: A 119 GLU cc_start: 0.9134 (tp30) cc_final: 0.8723 (tm-30) REVERT: A 120 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8978 (mm) REVERT: A 127 TRP cc_start: 0.7844 (t60) cc_final: 0.7300 (t-100) REVERT: A 166 ASP cc_start: 0.8302 (t0) cc_final: 0.7901 (t0) REVERT: A 219 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8541 (mt-10) REVERT: A 319 MET cc_start: 0.8219 (tpp) cc_final: 0.7766 (tpp) REVERT: A 364 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.7218 (ttp-110) REVERT: A 467 ILE cc_start: 0.6593 (OUTLIER) cc_final: 0.6206 (tt) REVERT: C 38 ARG cc_start: 0.9476 (ptm160) cc_final: 0.9266 (mtp-110) REVERT: C 39 VAL cc_start: 0.9589 (t) cc_final: 0.9256 (m) REVERT: C 62 GLN cc_start: 0.8582 (mp10) cc_final: 0.8276 (mp10) REVERT: C 101 GLU cc_start: 0.9260 (pm20) cc_final: 0.8972 (pm20) REVERT: D 24 GLN cc_start: 0.9379 (mm110) cc_final: 0.9138 (mm-40) REVERT: D 29 GLU cc_start: 0.9163 (mm-30) cc_final: 0.7937 (mp0) REVERT: D 31 VAL cc_start: 0.9552 (t) cc_final: 0.9348 (m) REVERT: D 37 VAL cc_start: 0.9310 (t) cc_final: 0.9032 (p) REVERT: D 42 LYS cc_start: 0.9247 (ttmm) cc_final: 0.8878 (ttpp) REVERT: D 61 GLU cc_start: 0.8424 (pp20) cc_final: 0.7942 (pp20) REVERT: D 62 GLN cc_start: 0.9215 (tp40) cc_final: 0.8205 (mp10) outliers start: 24 outliers final: 10 residues processed: 147 average time/residue: 1.0176 time to fit residues: 157.9919 Evaluate side-chains 135 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU 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 364 ARG Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 100 SER 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 40 optimal weight: 2.9990 chunk 57 optimal weight: 20.0000 chunk 83 optimal weight: 30.0000 chunk 47 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 144 ASN A 182 GLN C 48 ASN C 109 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.079490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.060118 restraints weight = 18431.371| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 3.72 r_work: 0.2675 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6322 Z= 0.229 Angle : 0.689 14.414 8623 Z= 0.326 Chirality : 0.043 0.226 1026 Planarity : 0.004 0.053 1095 Dihedral : 3.646 48.275 928 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.34 % Favored : 96.54 % Rotamer: Outliers : 3.36 % Allowed : 39.47 % Favored : 57.17 % 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: 2.61 (0.29), residues: 867 helix: 2.95 (0.25), residues: 410 sheet: 1.57 (0.38), residues: 200 loop : -0.23 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 211 HIS 0.012 0.002 HIS A 118 PHE 0.014 0.001 PHE C 30 TYR 0.007 0.001 TYR A 64 ARG 0.005 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 140 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 17 LEU cc_start: 0.8703 (pt) cc_final: 0.8326 (tm) REVERT: A 102 SER cc_start: 0.9590 (m) cc_final: 0.9357 (p) REVERT: A 119 GLU cc_start: 0.9142 (tp30) cc_final: 0.8772 (tm-30) REVERT: A 120 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8958 (mm) REVERT: A 123 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8420 (tmm) REVERT: A 127 TRP cc_start: 0.7878 (t60) cc_final: 0.7349 (t-100) REVERT: A 165 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7043 (mm-30) REVERT: A 166 ASP cc_start: 0.8455 (t0) cc_final: 0.7324 (t0) REVERT: A 324 PHE cc_start: 0.9330 (OUTLIER) cc_final: 0.8841 (t80) REVERT: C 38 ARG cc_start: 0.9463 (ptm160) cc_final: 0.9255 (mtp-110) REVERT: C 39 VAL cc_start: 0.9567 (t) cc_final: 0.9236 (m) REVERT: C 62 GLN cc_start: 0.8604 (mp10) cc_final: 0.8291 (mp10) REVERT: C 70 SER cc_start: 0.9706 (OUTLIER) cc_final: 0.9139 (p) REVERT: C 101 GLU cc_start: 0.9261 (pm20) cc_final: 0.8978 (pm20) REVERT: C 109 GLN cc_start: 0.9430 (OUTLIER) cc_final: 0.8770 (tm-30) REVERT: D 24 GLN cc_start: 0.9390 (mm110) cc_final: 0.9155 (mm-40) REVERT: D 29 GLU cc_start: 0.9193 (mm-30) cc_final: 0.7884 (mp0) REVERT: D 31 VAL cc_start: 0.9553 (t) cc_final: 0.9342 (m) REVERT: D 37 VAL cc_start: 0.9346 (t) cc_final: 0.9050 (p) REVERT: D 42 LYS cc_start: 0.9277 (ttmm) cc_final: 0.8888 (ttpp) REVERT: D 62 GLN cc_start: 0.9090 (tp40) cc_final: 0.8488 (mm-40) REVERT: D 119 ARG cc_start: 0.8848 (tpt90) cc_final: 0.8622 (tpp80) outliers start: 19 outliers final: 12 residues processed: 133 average time/residue: 1.1438 time to fit residues: 161.4837 Evaluate side-chains 133 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU 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 70 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 61 GLU 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 80 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 54 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 48 optimal weight: 0.0970 chunk 25 optimal weight: 0.9990 chunk 63 optimal weight: 50.0000 chunk 67 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 C 109 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.079716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.060851 restraints weight = 18398.984| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 3.70 r_work: 0.2682 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 6322 Z= 0.287 Angle : 1.087 59.190 8623 Z= 0.603 Chirality : 0.048 0.689 1026 Planarity : 0.005 0.082 1095 Dihedral : 3.725 48.236 928 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.34 % Favored : 96.42 % Rotamer: Outliers : 3.54 % Allowed : 40.00 % Favored : 56.46 % Cbeta Deviations : 0.12 % 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: 2.59 (0.29), residues: 867 helix: 2.95 (0.25), residues: 410 sheet: 1.55 (0.38), residues: 200 loop : -0.25 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 211 HIS 0.011 0.002 HIS A 118 PHE 0.015 0.001 PHE C 118 TYR 0.007 0.001 TYR A 64 ARG 0.004 0.000 ARG C 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4456.43 seconds wall clock time: 76 minutes 42.49 seconds (4602.49 seconds total)