Starting phenix.real_space_refine on Fri Dec 27 11:03:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8de7_27386/12_2024/8de7_27386.cif Found real_map, /net/cci-nas-00/data/ceres_data/8de7_27386/12_2024/8de7_27386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8de7_27386/12_2024/8de7_27386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8de7_27386/12_2024/8de7_27386.map" model { file = "/net/cci-nas-00/data/ceres_data/8de7_27386/12_2024/8de7_27386.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8de7_27386/12_2024/8de7_27386.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 K 3 8.98 5 S 16 5.16 5 C 2789 2.51 5 N 637 2.21 5 O 723 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4168 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2067 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 7, 'TRANS': 255} Chain: "A" Number of atoms: 2063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2063 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 255} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.27, per 1000 atoms: 0.78 Number of scatterers: 4168 At special positions: 0 Unit cell: (80.7, 79.624, 94.688, 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) K 3 19.00 S 16 16.00 O 723 8.00 N 637 7.00 C 2789 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS A 93 " 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: 1.20 Conformation dependent library (CDL) restraints added in 469.6 milliseconds 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 956 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 79.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'B' and resid 43 through 91 Proline residue: B 71 - end of helix Processing helix chain 'B' and resid 95 through 113 Processing helix chain 'B' and resid 128 through 142 Processing helix chain 'B' and resid 152 through 194 removed outlier: 3.738A pdb=" N ILE B 157 " --> pdb=" O GLU B 153 " (cutoff:3.500A) Proline residue: B 168 - end of helix removed outlier: 4.078A pdb=" N LYS B 194 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 223 Processing helix chain 'B' and resid 224 through 235 Processing helix chain 'B' and resid 237 through 251 removed outlier: 3.641A pdb=" N ILE B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 302 Processing helix chain 'A' and resid 43 through 91 Proline residue: A 71 - end of helix Processing helix chain 'A' and resid 95 through 113 Processing helix chain 'A' and resid 128 through 142 Processing helix chain 'A' and resid 152 through 197 Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 202 through 223 removed outlier: 3.888A pdb=" N ARG A 207 " --> pdb=" O GLN A 203 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A 221 " --> pdb=" O PHE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 234 Processing helix chain 'A' and resid 237 through 250 Processing helix chain 'A' and resid 270 through 301 removed outlier: 3.982A pdb=" N ALA A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR A 284 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS A 301 " --> pdb=" O ARG A 297 " (cutoff:3.500A) 334 hydrogen bonds defined for protein. 1002 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: 1.20 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1199 1.34 - 1.46: 807 1.46 - 1.58: 2240 1.58 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 4272 Sorted by residual: bond pdb=" C1B LMT B 401 " pdb=" O5B LMT B 401 " ideal model delta sigma weight residual 1.393 1.502 -0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C1' LMT B 401 " pdb=" O5' LMT B 401 " ideal model delta sigma weight residual 1.408 1.503 -0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C5' LMT B 401 " pdb=" O5' LMT B 401 " ideal model delta sigma weight residual 1.411 1.473 -0.062 2.00e-02 2.50e+03 9.76e+00 bond pdb=" C5B LMT B 401 " pdb=" O5B LMT B 401 " ideal model delta sigma weight residual 1.422 1.479 -0.057 2.00e-02 2.50e+03 8.18e+00 bond pdb=" C3B LMT B 401 " pdb=" O3B LMT B 401 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.89e+00 ... (remaining 4267 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 5578 2.51 - 5.02: 186 5.02 - 7.52: 34 7.52 - 10.03: 3 10.03 - 12.54: 2 Bond angle restraints: 5803 Sorted by residual: angle pdb=" N VAL A 197 " pdb=" CA VAL A 197 " pdb=" C VAL A 197 " ideal model delta sigma weight residual 110.62 114.52 -3.90 1.02e+00 9.61e-01 1.46e+01 angle pdb=" N GLY A 166 " pdb=" CA GLY A 166 " pdb=" C GLY A 166 " ideal model delta sigma weight residual 112.77 117.60 -4.83 1.28e+00 6.10e-01 1.42e+01 angle pdb=" CA LEU A 267 " pdb=" CB LEU A 267 " pdb=" CG LEU A 267 " ideal model delta sigma weight residual 116.30 128.84 -12.54 3.50e+00 8.16e-02 1.28e+01 angle pdb=" CA LEU B 169 " pdb=" CB LEU B 169 " pdb=" CG LEU B 169 " ideal model delta sigma weight residual 116.30 128.68 -12.38 3.50e+00 8.16e-02 1.25e+01 angle pdb=" CA THR B 152 " pdb=" CB THR B 152 " pdb=" CG2 THR B 152 " ideal model delta sigma weight residual 110.50 116.33 -5.83 1.70e+00 3.46e-01 1.18e+01 ... (remaining 5798 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.63: 2230 19.63 - 39.27: 194 39.27 - 58.90: 36 58.90 - 78.53: 5 78.53 - 98.16: 13 Dihedral angle restraints: 2478 sinusoidal: 982 harmonic: 1496 Sorted by residual: dihedral pdb=" CB CYS B 93 " pdb=" SG CYS B 93 " pdb=" SG CYS A 93 " pdb=" CB CYS A 93 " ideal model delta sinusoidal sigma weight residual -86.00 -165.74 79.74 1 1.00e+01 1.00e-02 7.89e+01 dihedral pdb=" O2B LMT B 401 " pdb=" C1B LMT B 401 " pdb=" C2B LMT B 401 " pdb=" O5B LMT B 401 " ideal model delta sinusoidal sigma weight residual -176.42 -78.26 -98.16 1 3.00e+01 1.11e-03 1.22e+01 dihedral pdb=" C3B LMT B 401 " pdb=" C1B LMT B 401 " pdb=" C2B LMT B 401 " pdb=" O5B LMT B 401 " ideal model delta sinusoidal sigma weight residual -53.08 43.42 -96.50 1 3.00e+01 1.11e-03 1.19e+01 ... (remaining 2475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 499 0.052 - 0.103: 125 0.103 - 0.155: 49 0.155 - 0.206: 7 0.206 - 0.258: 8 Chirality restraints: 688 Sorted by residual: chirality pdb=" CB THR A 138 " pdb=" CA THR A 138 " pdb=" OG1 THR A 138 " pdb=" CG2 THR A 138 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA GLN B 70 " pdb=" N GLN B 70 " pdb=" C GLN B 70 " pdb=" CB GLN B 70 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CG LEU B 169 " pdb=" CB LEU B 169 " pdb=" CD1 LEU B 169 " pdb=" CD2 LEU B 169 " both_signs ideal model delta sigma weight residual False -2.59 -2.84 0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 685 not shown) Planarity restraints: 692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 149 " -0.046 5.00e-02 4.00e+02 6.94e-02 7.70e+00 pdb=" N PRO B 150 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 150 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 150 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 115 " 0.046 5.00e-02 4.00e+02 6.86e-02 7.53e+00 pdb=" N PRO A 116 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 116 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 116 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 149 " 0.044 5.00e-02 4.00e+02 6.68e-02 7.13e+00 pdb=" N PRO A 150 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " 0.037 5.00e-02 4.00e+02 ... (remaining 689 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.87: 1466 2.87 - 3.44: 5212 3.44 - 4.01: 7477 4.01 - 4.57: 10627 4.57 - 5.14: 14643 Nonbonded interactions: 39425 Sorted by model distance: nonbonded pdb=" OG SER B 121 " pdb=" OG SER B 124 " model vdw 2.304 3.040 nonbonded pdb=" OE2 GLU A 234 " pdb=" OH TYR A 266 " model vdw 2.349 3.040 nonbonded pdb=" NZ LYS B 84 " pdb=" O PRO A 116 " model vdw 2.351 3.120 nonbonded pdb=" O ALA A 287 " pdb=" OG SER A 290 " model vdw 2.358 3.040 nonbonded pdb=" O ARG A 111 " pdb=" NE2 HIS A 151 " model vdw 2.380 3.120 ... (remaining 39420 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 41 through 301) selection = (chain 'B' and resid 41 through 301) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.240 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 4272 Z= 0.388 Angle : 1.051 12.541 5803 Z= 0.576 Chirality : 0.058 0.258 688 Planarity : 0.008 0.069 692 Dihedral : 16.507 98.164 1519 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.90 % Allowed : 0.22 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.08 (0.33), residues: 522 helix: 3.44 (0.22), residues: 402 sheet: None (None), residues: 0 loop : -0.10 (0.51), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 199 HIS 0.006 0.002 HIS B 151 PHE 0.023 0.003 PHE A 285 TYR 0.017 0.003 TYR B 266 ARG 0.005 0.001 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 251 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 LEU cc_start: 0.9398 (tp) cc_final: 0.9102 (tp) REVERT: B 82 GLN cc_start: 0.9328 (mm110) cc_final: 0.9022 (mm-40) REVERT: B 96 THR cc_start: 0.9353 (t) cc_final: 0.8967 (p) REVERT: B 99 LEU cc_start: 0.9722 (tp) cc_final: 0.9385 (tp) REVERT: B 101 ASP cc_start: 0.9448 (t0) cc_final: 0.9191 (m-30) REVERT: B 104 LYS cc_start: 0.9481 (ttmm) cc_final: 0.9227 (mtmm) REVERT: B 215 ILE cc_start: 0.9649 (mt) cc_final: 0.9306 (mt) REVERT: B 231 GLN cc_start: 0.8610 (tt0) cc_final: 0.8370 (tt0) REVERT: A 48 LEU cc_start: 0.9520 (tp) cc_final: 0.9291 (tp) REVERT: A 52 LEU cc_start: 0.9366 (mt) cc_final: 0.9164 (mt) REVERT: A 56 LEU cc_start: 0.9303 (tp) cc_final: 0.9048 (tp) REVERT: A 66 LYS cc_start: 0.8778 (ttmt) cc_final: 0.8385 (ttmm) REVERT: A 77 LYS cc_start: 0.9092 (mmmm) cc_final: 0.8857 (mmmm) REVERT: A 82 GLN cc_start: 0.9406 (tp40) cc_final: 0.9141 (mm-40) REVERT: A 95 GLN cc_start: 0.9193 (mm110) cc_final: 0.8622 (mm110) REVERT: A 104 LYS cc_start: 0.9540 (ttpp) cc_final: 0.9319 (mtmm) REVERT: A 105 GLN cc_start: 0.9524 (mm110) cc_final: 0.9259 (mm-40) REVERT: A 191 LYS cc_start: 0.8595 (mttp) cc_final: 0.8100 (ttmm) REVERT: A 196 PHE cc_start: 0.9018 (t80) cc_final: 0.8692 (t80) REVERT: A 216 LEU cc_start: 0.9372 (mp) cc_final: 0.9109 (mp) REVERT: A 225 LEU cc_start: 0.9268 (tp) cc_final: 0.9038 (tp) REVERT: A 269 TYR cc_start: 0.8095 (m-80) cc_final: 0.7592 (m-80) outliers start: 4 outliers final: 1 residues processed: 253 average time/residue: 0.1551 time to fit residues: 48.4073 Evaluate side-chains 213 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 0.0970 chunk 14 optimal weight: 2.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN ** A 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 GLN A 200 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4272 Z= 0.274 Angle : 0.771 12.217 5803 Z= 0.381 Chirality : 0.046 0.285 688 Planarity : 0.005 0.048 692 Dihedral : 9.241 59.133 612 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 3.82 % Allowed : 19.78 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.77 (0.35), residues: 522 helix: 3.22 (0.23), residues: 408 sheet: None (None), residues: 0 loop : -0.43 (0.55), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 277 HIS 0.005 0.001 HIS B 151 PHE 0.019 0.002 PHE A 244 TYR 0.015 0.002 TYR B 162 ARG 0.003 0.001 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 218 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 GLU cc_start: 0.8119 (tt0) cc_final: 0.7839 (tt0) REVERT: B 82 GLN cc_start: 0.9380 (mm110) cc_final: 0.9077 (mm-40) REVERT: B 98 GLU cc_start: 0.9380 (mp0) cc_final: 0.9148 (mp0) REVERT: B 101 ASP cc_start: 0.9474 (t0) cc_final: 0.9202 (m-30) REVERT: B 104 LYS cc_start: 0.9495 (ttmm) cc_final: 0.9230 (mtmm) REVERT: B 231 GLN cc_start: 0.8646 (tt0) cc_final: 0.8394 (tt0) REVERT: A 42 MET cc_start: 0.8398 (mmm) cc_final: 0.8188 (mmm) REVERT: A 52 LEU cc_start: 0.9428 (mt) cc_final: 0.9223 (mt) REVERT: A 56 LEU cc_start: 0.9320 (tp) cc_final: 0.9112 (tp) REVERT: A 104 LYS cc_start: 0.9574 (ttpp) cc_final: 0.9289 (mtmm) REVERT: A 216 LEU cc_start: 0.9371 (mp) cc_final: 0.9140 (mp) REVERT: A 269 TYR cc_start: 0.7929 (m-80) cc_final: 0.7641 (m-80) REVERT: A 297 ARG cc_start: 0.8958 (mtp85) cc_final: 0.8668 (mtp-110) outliers start: 17 outliers final: 8 residues processed: 221 average time/residue: 0.1363 time to fit residues: 38.1775 Evaluate side-chains 211 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 203 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 278 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 16 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 ASN A 232 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 4272 Z= 0.264 Angle : 0.748 10.859 5803 Z= 0.376 Chirality : 0.045 0.289 688 Planarity : 0.005 0.059 692 Dihedral : 7.441 48.124 611 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.37 % Allowed : 22.92 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.36 (0.35), residues: 522 helix: 2.99 (0.23), residues: 407 sheet: None (None), residues: 0 loop : -0.77 (0.55), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 277 HIS 0.005 0.001 HIS A 232 PHE 0.020 0.001 PHE A 158 TYR 0.018 0.002 TYR A 266 ARG 0.007 0.001 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 207 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 ASP cc_start: 0.9487 (t0) cc_final: 0.9251 (m-30) REVERT: B 104 LYS cc_start: 0.9496 (ttmm) cc_final: 0.9207 (mtmm) REVERT: B 231 GLN cc_start: 0.8588 (tt0) cc_final: 0.8227 (tt0) REVERT: B 289 LEU cc_start: 0.8826 (mp) cc_final: 0.8591 (mp) REVERT: A 42 MET cc_start: 0.8462 (mmm) cc_final: 0.8197 (mmm) REVERT: A 51 PHE cc_start: 0.9425 (t80) cc_final: 0.9202 (t80) REVERT: A 98 GLU cc_start: 0.8894 (pt0) cc_final: 0.8662 (pt0) REVERT: A 99 LEU cc_start: 0.9454 (pp) cc_final: 0.8863 (pp) REVERT: A 100 GLU cc_start: 0.9331 (mm-30) cc_final: 0.9079 (mm-30) REVERT: A 104 LYS cc_start: 0.9561 (ttpp) cc_final: 0.9246 (mtmm) REVERT: A 122 GLN cc_start: 0.8589 (pm20) cc_final: 0.8334 (pm20) REVERT: A 231 GLN cc_start: 0.8064 (tm-30) cc_final: 0.7860 (tm-30) REVERT: A 269 TYR cc_start: 0.7901 (m-80) cc_final: 0.7644 (m-80) outliers start: 15 outliers final: 8 residues processed: 212 average time/residue: 0.1409 time to fit residues: 38.0657 Evaluate side-chains 208 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 200 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 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 76 GLN A 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 4272 Z= 0.311 Angle : 0.759 8.532 5803 Z= 0.374 Chirality : 0.045 0.233 688 Planarity : 0.005 0.069 692 Dihedral : 6.329 45.574 611 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 5.62 % Allowed : 24.04 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.98 (0.36), residues: 522 helix: 2.72 (0.24), residues: 410 sheet: None (None), residues: 0 loop : -1.04 (0.58), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 275 HIS 0.003 0.001 HIS A 151 PHE 0.020 0.002 PHE B 158 TYR 0.012 0.002 TYR A 270 ARG 0.004 0.001 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 204 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9218 (mp) REVERT: B 82 GLN cc_start: 0.9404 (mm110) cc_final: 0.9040 (mm-40) REVERT: B 95 GLN cc_start: 0.9046 (mp10) cc_final: 0.8702 (mp10) REVERT: B 98 GLU cc_start: 0.9273 (mp0) cc_final: 0.8976 (mp0) REVERT: B 104 LYS cc_start: 0.9528 (ttmm) cc_final: 0.9254 (mtmm) REVERT: B 195 MET cc_start: 0.4450 (ttp) cc_final: 0.3987 (tpp) REVERT: B 231 GLN cc_start: 0.8609 (tt0) cc_final: 0.8207 (tt0) REVERT: B 270 TYR cc_start: 0.8608 (t80) cc_final: 0.8394 (t80) REVERT: B 289 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8656 (mp) REVERT: A 42 MET cc_start: 0.8463 (mmm) cc_final: 0.8256 (mmm) REVERT: A 51 PHE cc_start: 0.9422 (t80) cc_final: 0.9198 (t80) REVERT: A 104 LYS cc_start: 0.9574 (ttpp) cc_final: 0.9239 (mtmm) REVERT: A 122 GLN cc_start: 0.8617 (pm20) cc_final: 0.8266 (pm20) REVERT: A 151 HIS cc_start: 0.8439 (m90) cc_final: 0.8079 (m170) REVERT: A 231 GLN cc_start: 0.8086 (tm-30) cc_final: 0.7814 (tm-30) REVERT: A 269 TYR cc_start: 0.7967 (m-80) cc_final: 0.7464 (m-80) outliers start: 25 outliers final: 14 residues processed: 210 average time/residue: 0.1393 time to fit residues: 37.1946 Evaluate side-chains 216 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 200 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 12 optimal weight: 0.4980 chunk 16 optimal weight: 5.9990 chunk 9 optimal weight: 0.1980 chunk 29 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4272 Z= 0.230 Angle : 0.762 8.182 5803 Z= 0.372 Chirality : 0.044 0.204 688 Planarity : 0.005 0.065 692 Dihedral : 5.969 43.669 611 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.15 % Allowed : 30.79 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.79 (0.36), residues: 522 helix: 2.57 (0.24), residues: 410 sheet: None (None), residues: 0 loop : -1.01 (0.60), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 44 HIS 0.003 0.001 HIS A 91 PHE 0.028 0.002 PHE A 196 TYR 0.013 0.002 TYR A 284 ARG 0.006 0.001 ARG A 297 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 214 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 GLN cc_start: 0.9380 (mm110) cc_final: 0.9003 (tp40) REVERT: B 83 GLU cc_start: 0.8797 (pp20) cc_final: 0.8515 (pp20) REVERT: B 101 ASP cc_start: 0.9483 (t70) cc_final: 0.9257 (m-30) REVERT: B 103 VAL cc_start: 0.9479 (t) cc_final: 0.9266 (m) REVERT: B 104 LYS cc_start: 0.9529 (ttmm) cc_final: 0.9248 (mtmm) REVERT: B 195 MET cc_start: 0.4099 (ttp) cc_final: 0.3805 (tpp) REVERT: B 231 GLN cc_start: 0.8593 (tt0) cc_final: 0.8214 (tt0) REVERT: B 289 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8671 (mp) REVERT: A 82 GLN cc_start: 0.9391 (tp40) cc_final: 0.9080 (mm-40) REVERT: A 104 LYS cc_start: 0.9572 (ttpp) cc_final: 0.9247 (mtmm) REVERT: A 122 GLN cc_start: 0.8671 (pm20) cc_final: 0.8303 (pm20) REVERT: A 151 HIS cc_start: 0.8430 (m90) cc_final: 0.7894 (m90) REVERT: A 231 GLN cc_start: 0.8101 (tm-30) cc_final: 0.7787 (tm-30) REVERT: A 269 TYR cc_start: 0.7824 (m-80) cc_final: 0.7620 (m-80) outliers start: 14 outliers final: 11 residues processed: 216 average time/residue: 0.1391 time to fit residues: 38.2202 Evaluate side-chains 217 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 205 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 282 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 23 optimal weight: 0.3980 chunk 4 optimal weight: 0.7980 chunk 16 optimal weight: 0.1980 chunk 26 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 5 optimal weight: 0.4980 chunk 28 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 4272 Z= 0.241 Angle : 0.812 13.736 5803 Z= 0.388 Chirality : 0.044 0.222 688 Planarity : 0.005 0.064 692 Dihedral : 5.762 49.537 611 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.72 % Allowed : 32.13 % Favored : 63.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.67 (0.36), residues: 522 helix: 2.46 (0.24), residues: 410 sheet: None (None), residues: 0 loop : -0.98 (0.61), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 44 HIS 0.003 0.001 HIS A 151 PHE 0.020 0.001 PHE A 51 TYR 0.013 0.002 TYR B 270 ARG 0.006 0.001 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 208 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ARG cc_start: 0.8958 (mtp-110) cc_final: 0.8748 (ttp-110) REVERT: B 101 ASP cc_start: 0.9481 (t70) cc_final: 0.9231 (m-30) REVERT: B 103 VAL cc_start: 0.9471 (t) cc_final: 0.9260 (m) REVERT: B 104 LYS cc_start: 0.9519 (ttmm) cc_final: 0.9240 (mtmm) REVERT: B 179 ASP cc_start: 0.7510 (OUTLIER) cc_final: 0.7297 (p0) REVERT: B 195 MET cc_start: 0.4025 (ttp) cc_final: 0.3751 (tpp) REVERT: B 231 GLN cc_start: 0.8580 (tt0) cc_final: 0.8192 (tt0) REVERT: B 240 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7800 (pt0) REVERT: B 289 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8657 (mp) REVERT: A 51 PHE cc_start: 0.9401 (t80) cc_final: 0.9183 (t80) REVERT: A 79 ARG cc_start: 0.9180 (OUTLIER) cc_final: 0.8977 (ptm-80) REVERT: A 98 GLU cc_start: 0.9428 (mp0) cc_final: 0.9042 (pm20) REVERT: A 104 LYS cc_start: 0.9563 (ttpp) cc_final: 0.9291 (mtmm) REVERT: A 122 GLN cc_start: 0.8665 (pm20) cc_final: 0.8311 (pm20) REVERT: A 151 HIS cc_start: 0.8399 (m90) cc_final: 0.8073 (m170) REVERT: A 231 GLN cc_start: 0.8098 (tm-30) cc_final: 0.7767 (tm-30) outliers start: 21 outliers final: 16 residues processed: 211 average time/residue: 0.1388 time to fit residues: 37.4334 Evaluate side-chains 220 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 201 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 23 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 4272 Z= 0.270 Angle : 0.831 12.190 5803 Z= 0.404 Chirality : 0.044 0.175 688 Planarity : 0.005 0.066 692 Dihedral : 5.782 50.298 611 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.49 % Allowed : 35.73 % Favored : 59.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.56 (0.36), residues: 522 helix: 2.37 (0.24), residues: 410 sheet: None (None), residues: 0 loop : -0.94 (0.60), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 44 HIS 0.004 0.001 HIS A 91 PHE 0.018 0.001 PHE B 158 TYR 0.020 0.002 TYR B 270 ARG 0.006 0.001 ARG A 297 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ARG cc_start: 0.8984 (mtp-110) cc_final: 0.8767 (ttp-110) REVERT: B 82 GLN cc_start: 0.9384 (mm110) cc_final: 0.9019 (tp40) REVERT: B 101 ASP cc_start: 0.9473 (t70) cc_final: 0.9243 (m-30) REVERT: B 104 LYS cc_start: 0.9522 (ttmm) cc_final: 0.9245 (mtmm) REVERT: B 195 MET cc_start: 0.4164 (ttp) cc_final: 0.3780 (tpp) REVERT: B 231 GLN cc_start: 0.8610 (tt0) cc_final: 0.8207 (tt0) REVERT: B 240 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7807 (pt0) REVERT: B 289 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8675 (mp) REVERT: A 51 PHE cc_start: 0.9406 (t80) cc_final: 0.9188 (t80) REVERT: A 79 ARG cc_start: 0.9198 (OUTLIER) cc_final: 0.8993 (ptm-80) REVERT: A 100 GLU cc_start: 0.9290 (mm-30) cc_final: 0.9013 (mm-30) REVERT: A 104 LYS cc_start: 0.9556 (ttpp) cc_final: 0.9323 (ttmm) REVERT: A 122 GLN cc_start: 0.8722 (pm20) cc_final: 0.8410 (pm20) REVERT: A 151 HIS cc_start: 0.8462 (m90) cc_final: 0.8141 (m170) REVERT: A 172 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.7861 (t80) REVERT: A 231 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7764 (tm-30) outliers start: 20 outliers final: 13 residues processed: 205 average time/residue: 0.1405 time to fit residues: 36.8895 Evaluate side-chains 217 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 201 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 282 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 14 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 4272 Z= 0.258 Angle : 0.873 13.926 5803 Z= 0.420 Chirality : 0.046 0.277 688 Planarity : 0.005 0.063 692 Dihedral : 5.726 52.742 611 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.94 % Allowed : 35.28 % Favored : 59.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.36), residues: 522 helix: 2.27 (0.24), residues: 410 sheet: None (None), residues: 0 loop : -0.94 (0.61), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 127 HIS 0.003 0.001 HIS A 151 PHE 0.032 0.002 PHE A 196 TYR 0.023 0.002 TYR B 270 ARG 0.004 0.001 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ARG cc_start: 0.9002 (mtp-110) cc_final: 0.8781 (ttp-110) REVERT: B 82 GLN cc_start: 0.9369 (mm110) cc_final: 0.8990 (tp40) REVERT: B 95 GLN cc_start: 0.8717 (mp10) cc_final: 0.8483 (mp10) REVERT: B 101 ASP cc_start: 0.9468 (t70) cc_final: 0.9176 (m-30) REVERT: B 104 LYS cc_start: 0.9531 (ttmm) cc_final: 0.9244 (mtmm) REVERT: B 195 MET cc_start: 0.4183 (ttp) cc_final: 0.3870 (tpp) REVERT: B 240 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7874 (pt0) REVERT: B 289 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8671 (mp) REVERT: A 42 MET cc_start: 0.8363 (mmm) cc_final: 0.8163 (mmp) REVERT: A 51 PHE cc_start: 0.9394 (t80) cc_final: 0.9177 (t80) REVERT: A 95 GLN cc_start: 0.8729 (mp10) cc_final: 0.8470 (mp10) REVERT: A 100 GLU cc_start: 0.9297 (mm-30) cc_final: 0.8960 (mm-30) REVERT: A 104 LYS cc_start: 0.9568 (ttpp) cc_final: 0.9360 (ttmm) REVERT: A 122 GLN cc_start: 0.8744 (pm20) cc_final: 0.8391 (pm20) REVERT: A 151 HIS cc_start: 0.8422 (m90) cc_final: 0.8115 (m170) REVERT: A 172 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.7837 (t80) REVERT: A 231 GLN cc_start: 0.8108 (tm-30) cc_final: 0.7775 (tm-30) outliers start: 22 outliers final: 16 residues processed: 208 average time/residue: 0.1430 time to fit residues: 38.0079 Evaluate side-chains 219 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 201 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 47 optimal weight: 0.4980 chunk 41 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4272 Z= 0.272 Angle : 0.914 13.813 5803 Z= 0.440 Chirality : 0.046 0.237 688 Planarity : 0.005 0.065 692 Dihedral : 5.758 53.153 611 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.04 % Allowed : 36.40 % Favored : 59.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.32 (0.36), residues: 522 helix: 2.20 (0.24), residues: 409 sheet: None (None), residues: 0 loop : -0.99 (0.60), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 127 HIS 0.004 0.001 HIS A 91 PHE 0.018 0.001 PHE B 158 TYR 0.025 0.003 TYR B 270 ARG 0.007 0.001 ARG A 297 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 206 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ARG cc_start: 0.9067 (mtp-110) cc_final: 0.8825 (ttp-110) REVERT: B 82 GLN cc_start: 0.9369 (mm110) cc_final: 0.8963 (tp40) REVERT: B 104 LYS cc_start: 0.9530 (ttmm) cc_final: 0.9245 (mtmm) REVERT: B 195 MET cc_start: 0.4251 (ttp) cc_final: 0.3878 (tpp) REVERT: B 231 GLN cc_start: 0.8626 (tt0) cc_final: 0.8247 (tt0) REVERT: A 51 PHE cc_start: 0.9389 (t80) cc_final: 0.9152 (t80) REVERT: A 95 GLN cc_start: 0.8807 (mp10) cc_final: 0.8564 (mp10) REVERT: A 100 GLU cc_start: 0.9282 (mm-30) cc_final: 0.8930 (mm-30) REVERT: A 122 GLN cc_start: 0.8773 (pm20) cc_final: 0.8422 (pm20) REVERT: A 151 HIS cc_start: 0.8453 (m90) cc_final: 0.8145 (m170) REVERT: A 172 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.7850 (t80) REVERT: A 207 ARG cc_start: 0.8595 (tmt170) cc_final: 0.8319 (tpt90) REVERT: A 231 GLN cc_start: 0.8140 (tm-30) cc_final: 0.7803 (tm-30) outliers start: 18 outliers final: 16 residues processed: 207 average time/residue: 0.1388 time to fit residues: 36.8016 Evaluate side-chains 218 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 201 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 32 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 38 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 11 optimal weight: 0.0980 chunk 41 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4272 Z= 0.266 Angle : 0.946 14.190 5803 Z= 0.453 Chirality : 0.047 0.227 688 Planarity : 0.005 0.065 692 Dihedral : 5.865 54.885 611 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.60 % Allowed : 38.43 % Favored : 57.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.17 (0.36), residues: 522 helix: 2.08 (0.25), residues: 408 sheet: None (None), residues: 0 loop : -0.95 (0.60), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 127 HIS 0.003 0.001 HIS A 151 PHE 0.055 0.002 PHE A 196 TYR 0.024 0.002 TYR B 270 ARG 0.003 0.001 ARG B 79 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 201 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ARG cc_start: 0.9057 (mtp-110) cc_final: 0.8809 (ttp-110) REVERT: B 82 GLN cc_start: 0.9364 (mm110) cc_final: 0.8971 (tp40) REVERT: B 101 ASP cc_start: 0.9476 (t70) cc_final: 0.9210 (m-30) REVERT: B 104 LYS cc_start: 0.9542 (ttmm) cc_final: 0.9256 (mtmm) REVERT: B 195 MET cc_start: 0.4343 (ttp) cc_final: 0.3893 (tpp) REVERT: B 231 GLN cc_start: 0.8609 (tt0) cc_final: 0.8275 (tt0) REVERT: A 51 PHE cc_start: 0.9380 (t80) cc_final: 0.9161 (t80) REVERT: A 100 GLU cc_start: 0.9314 (mm-30) cc_final: 0.8907 (mm-30) REVERT: A 122 GLN cc_start: 0.8786 (pm20) cc_final: 0.8438 (pm20) REVERT: A 151 HIS cc_start: 0.8434 (m90) cc_final: 0.8131 (m170) REVERT: A 172 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7842 (t80) REVERT: A 207 ARG cc_start: 0.8611 (tmt170) cc_final: 0.8318 (tpt90) REVERT: A 231 GLN cc_start: 0.8156 (tm-30) cc_final: 0.7817 (tm-30) outliers start: 16 outliers final: 15 residues processed: 202 average time/residue: 0.1334 time to fit residues: 34.6266 Evaluate side-chains 209 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 193 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 2 optimal weight: 0.0770 chunk 29 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.150028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.100651 restraints weight = 7240.432| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 4.21 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4272 Z= 0.272 Angle : 0.970 13.959 5803 Z= 0.465 Chirality : 0.048 0.320 688 Planarity : 0.005 0.063 692 Dihedral : 6.100 57.310 611 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.82 % Allowed : 38.20 % Favored : 57.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.19 (0.36), residues: 522 helix: 2.12 (0.25), residues: 399 sheet: None (None), residues: 0 loop : -0.84 (0.57), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 277 HIS 0.003 0.001 HIS A 151 PHE 0.025 0.002 PHE B 51 TYR 0.024 0.002 TYR B 270 ARG 0.006 0.001 ARG A 297 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1370.05 seconds wall clock time: 25 minutes 32.98 seconds (1532.98 seconds total)