Starting phenix.real_space_refine on Sun Mar 10 18:59:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de7_27386/03_2024/8de7_27386_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de7_27386/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de7_27386/03_2024/8de7_27386.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de7_27386/03_2024/8de7_27386.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de7_27386/03_2024/8de7_27386_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de7_27386/03_2024/8de7_27386_updated.pdb" } 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 Residue "B PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 240": "OE1" <-> "OE2" Residue "B PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 240": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 2.85, per 1000 atoms: 0.68 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.99 Conformation dependent library (CDL) restraints added in 791.1 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... running ksdssp... Secondary structure from input PDB file: 16 helices and 0 sheets defined 73.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'B' and resid 44 through 90 Proline residue: B 71 - end of helix Processing helix chain 'B' and resid 96 through 112 Processing helix chain 'B' and resid 129 through 141 Processing helix chain 'B' and resid 153 through 193 removed outlier: 3.738A pdb=" N ILE B 157 " --> pdb=" O GLU B 153 " (cutoff:3.500A) Proline residue: B 168 - end of helix Processing helix chain 'B' and resid 203 through 222 Processing helix chain 'B' and resid 225 through 234 Processing helix chain 'B' and resid 238 through 250 removed outlier: 3.641A pdb=" N ILE B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 301 Processing helix chain 'A' and resid 44 through 90 Proline residue: A 71 - end of helix Processing helix chain 'A' and resid 96 through 112 Processing helix chain 'A' and resid 129 through 141 Processing helix chain 'A' and resid 153 through 196 Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 203 through 222 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 224 through 233 Processing helix chain 'A' and resid 238 through 250 Processing helix chain 'A' and resid 271 through 300 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) 305 hydrogen bonds defined for protein. 915 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: 1.04 Time building geometry restraints manager: 2.09 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: 99.25 - 106.21: 82 106.21 - 113.16: 2330 113.16 - 120.12: 1552 120.12 - 127.08: 1781 127.08 - 134.04: 58 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: 1474 2.87 - 3.44: 5238 3.44 - 4.01: 7531 4.01 - 4.57: 10655 4.57 - 5.14: 14643 Nonbonded interactions: 39541 Sorted by model distance: nonbonded pdb=" OG SER B 121 " pdb=" OG SER B 124 " model vdw 2.304 2.440 nonbonded pdb=" OE2 GLU A 234 " pdb=" OH TYR A 266 " model vdw 2.349 2.440 nonbonded pdb=" NZ LYS B 84 " pdb=" O PRO A 116 " model vdw 2.351 2.520 nonbonded pdb=" O ALA A 287 " pdb=" OG SER A 290 " model vdw 2.358 2.440 nonbonded pdb=" O ARG A 111 " pdb=" NE2 HIS A 151 " model vdw 2.380 2.520 ... (remaining 39536 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 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: 1.680 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.480 Find NCS groups from input model: 0.240 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: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.880 ------------------------------------------------------------------------------- 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= 0.390 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 fitting. rotamer outliers: 4 poor density : 251 time to evaluate : 0.472 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: 0.1538 time to fit residues: 48.0946 Evaluate side-chains 213 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 212 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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: 2.9990 chunk 39 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN ** A 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4272 Z= 0.266 Angle : 0.750 11.768 5803 Z= 0.367 Chirality : 0.044 0.300 688 Planarity : 0.005 0.046 692 Dihedral : 9.066 57.190 612 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 3.37 % Allowed : 20.22 % 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: 3.74 (0.34), residues: 522 helix: 3.27 (0.23), residues: 403 sheet: None (None), residues: 0 loop : -0.54 (0.51), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 277 HIS 0.003 0.001 HIS A 91 PHE 0.019 0.002 PHE B 51 TYR 0.015 0.002 TYR B 162 ARG 0.004 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 232 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 217 time to evaluate : 0.479 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: 0.8153 (tt0) cc_final: 0.7896 (tt0) REVERT: B 82 GLN cc_start: 0.9396 (mm110) cc_final: 0.9041 (mm-40) REVERT: B 98 GLU cc_start: 0.9393 (mp0) cc_final: 0.9139 (mp0) REVERT: B 104 LYS cc_start: 0.9466 (ttmm) cc_final: 0.9188 (mtmm) REVERT: B 151 HIS cc_start: 0.7689 (m90) cc_final: 0.7383 (m90) REVERT: B 193 GLU cc_start: 0.9379 (tp30) cc_final: 0.9137 (tp30) REVERT: B 231 GLN cc_start: 0.8631 (tt0) cc_final: 0.8408 (tt0) REVERT: A 48 LEU cc_start: 0.9514 (tp) cc_final: 0.9296 (tp) REVERT: A 52 LEU cc_start: 0.9416 (mt) cc_final: 0.9215 (mt) REVERT: A 56 LEU cc_start: 0.9311 (tp) cc_final: 0.9105 (tp) REVERT: A 99 LEU cc_start: 0.9521 (pp) cc_final: 0.8668 (pp) REVERT: A 100 GLU cc_start: 0.9329 (mm-30) cc_final: 0.9040 (mm-30) REVERT: A 104 LYS cc_start: 0.9574 (ttpp) cc_final: 0.9285 (mtmm) REVERT: A 216 LEU cc_start: 0.9401 (mp) cc_final: 0.9182 (mp) REVERT: A 269 TYR cc_start: 0.7953 (m-80) cc_final: 0.7652 (m-80) REVERT: A 297 ARG cc_start: 0.8957 (mtp85) cc_final: 0.8648 (mtp85) outliers start: 15 outliers final: 7 residues processed: 219 average time/residue: 0.1377 time to fit residues: 38.1935 Evaluate side-chains 210 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 203 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 32 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 16 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3763 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= 0.256 Angle : 0.707 9.432 5803 Z= 0.350 Chirality : 0.043 0.297 688 Planarity : 0.004 0.038 692 Dihedral : 7.619 50.635 611 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.82 % Allowed : 23.82 % Favored : 72.36 % 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: 3.51 (0.35), residues: 522 helix: 3.09 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -0.58 (0.53), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 277 HIS 0.005 0.001 HIS A 91 PHE 0.021 0.002 PHE A 158 TYR 0.020 0.002 TYR A 266 ARG 0.004 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 226 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 209 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 GLU cc_start: 0.8258 (tt0) cc_final: 0.7956 (tt0) REVERT: B 99 LEU cc_start: 0.9684 (tp) cc_final: 0.9481 (tp) REVERT: B 100 GLU cc_start: 0.9230 (mm-30) cc_final: 0.8933 (mm-30) REVERT: B 103 VAL cc_start: 0.9474 (t) cc_final: 0.9244 (m) REVERT: B 104 LYS cc_start: 0.9471 (ttmm) cc_final: 0.9173 (mtmm) REVERT: B 231 GLN cc_start: 0.8606 (tt0) cc_final: 0.8294 (tt0) REVERT: B 289 LEU cc_start: 0.8782 (mp) cc_final: 0.8523 (mp) REVERT: A 44 TRP cc_start: 0.6738 (p-90) cc_final: 0.6515 (p90) REVERT: A 48 LEU cc_start: 0.9522 (tp) cc_final: 0.9305 (tp) REVERT: A 52 LEU cc_start: 0.9428 (mt) cc_final: 0.9216 (mt) REVERT: A 95 GLN cc_start: 0.8948 (mm110) cc_final: 0.8653 (mm110) REVERT: A 98 GLU cc_start: 0.8815 (pt0) cc_final: 0.8457 (pt0) REVERT: A 100 GLU cc_start: 0.9338 (mm-30) cc_final: 0.8993 (mm-30) REVERT: A 104 LYS cc_start: 0.9561 (ttpp) cc_final: 0.9265 (mtmm) REVERT: A 122 GLN cc_start: 0.8832 (pm20) cc_final: 0.8556 (pm20) REVERT: A 187 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8465 (tttm) REVERT: A 231 GLN cc_start: 0.8118 (tm-30) cc_final: 0.7907 (tm-30) REVERT: A 269 TYR cc_start: 0.7969 (m-80) cc_final: 0.7657 (m-80) outliers start: 17 outliers final: 10 residues processed: 213 average time/residue: 0.1016 time to fit residues: 27.6882 Evaluate side-chains 212 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 201 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 296 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 187 LYS 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: 6.9990 chunk 22 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 4272 Z= 0.274 Angle : 0.714 7.481 5803 Z= 0.350 Chirality : 0.043 0.230 688 Planarity : 0.004 0.040 692 Dihedral : 6.330 41.780 611 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.49 % Allowed : 26.07 % Favored : 69.44 % 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: 3.20 (0.35), residues: 522 helix: 2.91 (0.23), residues: 403 sheet: None (None), residues: 0 loop : -0.82 (0.52), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 277 HIS 0.004 0.001 HIS A 232 PHE 0.021 0.002 PHE A 158 TYR 0.013 0.002 TYR A 266 ARG 0.006 0.001 ARG A 297 *********************** 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 223 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 203 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9229 (mp) REVERT: B 82 GLN cc_start: 0.9401 (mm110) cc_final: 0.9030 (mm-40) REVERT: B 100 GLU cc_start: 0.9233 (mm-30) cc_final: 0.8969 (mm-30) REVERT: B 101 ASP cc_start: 0.9460 (t0) cc_final: 0.9191 (m-30) REVERT: B 103 VAL cc_start: 0.9486 (t) cc_final: 0.9283 (m) REVERT: B 104 LYS cc_start: 0.9471 (ttmm) cc_final: 0.9200 (mtmm) REVERT: B 195 MET cc_start: 0.4087 (ttp) cc_final: 0.3624 (tpp) REVERT: B 231 GLN cc_start: 0.8614 (tt0) cc_final: 0.8323 (tt0) REVERT: A 44 TRP cc_start: 0.6732 (p-90) cc_final: 0.6527 (p90) REVERT: A 48 LEU cc_start: 0.9534 (tp) cc_final: 0.9310 (tp) REVERT: A 95 GLN cc_start: 0.8958 (mm110) cc_final: 0.8693 (mm110) REVERT: A 98 GLU cc_start: 0.8820 (pt0) cc_final: 0.8441 (pt0) REVERT: A 100 GLU cc_start: 0.9374 (mm-30) cc_final: 0.9001 (mm-30) REVERT: A 104 LYS cc_start: 0.9575 (ttpp) cc_final: 0.9287 (mtmm) REVERT: A 195 MET cc_start: 0.8899 (tmm) cc_final: 0.8572 (tmm) REVERT: A 231 GLN cc_start: 0.8093 (tm-30) cc_final: 0.7816 (tm-30) REVERT: A 269 TYR cc_start: 0.7969 (m-80) cc_final: 0.7682 (m-80) outliers start: 20 outliers final: 11 residues processed: 206 average time/residue: 0.1347 time to fit residues: 35.4641 Evaluate side-chains 213 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 201 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 241 SER 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 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: 0.5980 chunk 42 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 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: 0.7977 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4272 Z= 0.254 Angle : 0.721 7.501 5803 Z= 0.353 Chirality : 0.041 0.196 688 Planarity : 0.004 0.043 692 Dihedral : 5.984 41.361 611 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.49 % Allowed : 29.21 % Favored : 66.29 % 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: 2.99 (0.35), residues: 522 helix: 2.76 (0.24), residues: 402 sheet: None (None), residues: 0 loop : -0.90 (0.53), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 275 HIS 0.005 0.001 HIS A 91 PHE 0.020 0.001 PHE A 158 TYR 0.015 0.002 TYR B 57 ARG 0.006 0.001 ARG B 79 *********************** 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 227 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 207 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 GLN cc_start: 0.9395 (mm110) cc_final: 0.9068 (tp40) REVERT: B 100 GLU cc_start: 0.9212 (mm-30) cc_final: 0.8959 (mm-30) REVERT: B 101 ASP cc_start: 0.9466 (t0) cc_final: 0.9229 (m-30) REVERT: B 104 LYS cc_start: 0.9469 (ttmm) cc_final: 0.9193 (mtmm) REVERT: B 195 MET cc_start: 0.4099 (ttp) cc_final: 0.3724 (tpp) REVERT: B 231 GLN cc_start: 0.8601 (tt0) cc_final: 0.8307 (tt0) REVERT: A 44 TRP cc_start: 0.6791 (p-90) cc_final: 0.6571 (p90) REVERT: A 95 GLN cc_start: 0.8969 (mm110) cc_final: 0.8721 (mm110) REVERT: A 98 GLU cc_start: 0.8820 (pt0) cc_final: 0.8425 (pt0) REVERT: A 100 GLU cc_start: 0.9371 (mm-30) cc_final: 0.9010 (mm-30) REVERT: A 104 LYS cc_start: 0.9572 (ttpp) cc_final: 0.9273 (mtmm) REVERT: A 228 LEU cc_start: 0.9322 (mm) cc_final: 0.9109 (mm) REVERT: A 231 GLN cc_start: 0.8088 (tm-30) cc_final: 0.7789 (tm-30) REVERT: A 269 TYR cc_start: 0.7987 (m-80) cc_final: 0.7697 (m-80) outliers start: 20 outliers final: 17 residues processed: 211 average time/residue: 0.1329 time to fit residues: 35.7874 Evaluate side-chains 217 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 200 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 278 ILE 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 180 GLN Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 chunk 23 optimal weight: 0.0980 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 36 optimal weight: 0.3980 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 180 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4272 Z= 0.244 Angle : 0.764 10.998 5803 Z= 0.365 Chirality : 0.041 0.185 688 Planarity : 0.004 0.047 692 Dihedral : 5.885 45.590 611 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.49 % Allowed : 33.26 % Favored : 62.25 % 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: 2.83 (0.35), residues: 522 helix: 2.66 (0.24), residues: 399 sheet: None (None), residues: 0 loop : -0.92 (0.54), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 275 HIS 0.003 0.001 HIS A 91 PHE 0.021 0.001 PHE B 51 TYR 0.017 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 221 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 201 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: B 82 GLN cc_start: 0.9370 (mm110) cc_final: 0.9039 (tp40) REVERT: B 104 LYS cc_start: 0.9492 (ttmm) cc_final: 0.9187 (mtmm) REVERT: B 195 MET cc_start: 0.4005 (ttp) cc_final: 0.3604 (tpp) REVERT: B 231 GLN cc_start: 0.8608 (tt0) cc_final: 0.8307 (tt0) REVERT: A 44 TRP cc_start: 0.6697 (p-90) cc_final: 0.6490 (p90) REVERT: A 95 GLN cc_start: 0.8980 (mm110) cc_final: 0.8720 (mm110) REVERT: A 98 GLU cc_start: 0.8815 (pt0) cc_final: 0.8462 (pt0) REVERT: A 100 GLU cc_start: 0.9378 (mm-30) cc_final: 0.9025 (mm-30) REVERT: A 104 LYS cc_start: 0.9563 (ttpp) cc_final: 0.9266 (mtmm) REVERT: A 172 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7830 (t80) REVERT: A 228 LEU cc_start: 0.9334 (mm) cc_final: 0.9067 (mm) REVERT: A 231 GLN cc_start: 0.8110 (tm-30) cc_final: 0.7789 (tm-30) REVERT: A 269 TYR cc_start: 0.7994 (m-80) cc_final: 0.7707 (m-80) outliers start: 20 outliers final: 18 residues processed: 204 average time/residue: 0.1356 time to fit residues: 35.2402 Evaluate side-chains 219 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 200 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 149 SER 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 237 SER Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain A residue 50 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 172 PHE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 264 ILE 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: 1.9990 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 15 optimal weight: 9.9990 chunk 9 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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: 0.7978 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4272 Z= 0.261 Angle : 0.769 10.291 5803 Z= 0.372 Chirality : 0.042 0.181 688 Planarity : 0.004 0.051 692 Dihedral : 6.138 49.870 611 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 5.84 % Allowed : 34.38 % 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: 2.72 (0.35), residues: 522 helix: 2.58 (0.24), residues: 398 sheet: None (None), residues: 0 loop : -0.90 (0.55), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 275 HIS 0.003 0.001 HIS A 91 PHE 0.025 0.001 PHE A 158 TYR 0.016 0.002 TYR B 57 ARG 0.007 0.001 ARG B 79 *********************** 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 229 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 203 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 82 GLN cc_start: 0.9378 (mm110) cc_final: 0.9038 (tp40) REVERT: B 100 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8658 (mp0) REVERT: B 104 LYS cc_start: 0.9502 (ttmm) cc_final: 0.9207 (mtmm) REVERT: B 231 GLN cc_start: 0.8621 (tt0) cc_final: 0.8237 (tt0) REVERT: A 44 TRP cc_start: 0.6741 (p-90) cc_final: 0.6531 (p90) REVERT: A 79 ARG cc_start: 0.9211 (OUTLIER) cc_final: 0.8869 (ptm160) REVERT: A 82 GLN cc_start: 0.9396 (tp40) cc_final: 0.9084 (mm-40) REVERT: A 95 GLN cc_start: 0.8951 (mm110) cc_final: 0.8715 (mm110) REVERT: A 98 GLU cc_start: 0.8833 (pt0) cc_final: 0.8306 (pt0) REVERT: A 100 GLU cc_start: 0.9375 (mm-30) cc_final: 0.9077 (mm-30) REVERT: A 104 LYS cc_start: 0.9558 (ttpp) cc_final: 0.9278 (mtmm) REVERT: A 172 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7867 (t80) REVERT: A 228 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9121 (mm) REVERT: A 231 GLN cc_start: 0.8145 (tm-30) cc_final: 0.7814 (tm-30) outliers start: 26 outliers final: 21 residues processed: 208 average time/residue: 0.1353 time to fit residues: 35.9772 Evaluate side-chains 222 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 198 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 149 SER 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 237 SER Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 79 ARG 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 228 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 45 optimal weight: 0.0970 chunk 48 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 36 optimal weight: 0.0470 chunk 14 optimal weight: 0.8980 overall best weight: 0.4076 ------------------------------------------------------------------------------- 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: 0.7952 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4272 Z= 0.233 Angle : 0.817 12.153 5803 Z= 0.390 Chirality : 0.042 0.162 688 Planarity : 0.004 0.052 692 Dihedral : 5.901 54.114 611 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.72 % Allowed : 36.63 % Favored : 58.65 % 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: 2.51 (0.36), residues: 522 helix: 2.39 (0.24), residues: 398 sheet: None (None), residues: 0 loop : -0.82 (0.55), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 277 HIS 0.003 0.001 HIS B 151 PHE 0.025 0.001 PHE A 158 TYR 0.013 0.002 TYR B 284 ARG 0.008 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 225 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 204 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 GLN cc_start: 0.9366 (mm110) cc_final: 0.9024 (tp40) REVERT: B 101 ASP cc_start: 0.8918 (m-30) cc_final: 0.8562 (m-30) REVERT: B 104 LYS cc_start: 0.9506 (ttmm) cc_final: 0.9175 (mtmm) REVERT: B 231 GLN cc_start: 0.8594 (tt0) cc_final: 0.8216 (tt0) REVERT: A 79 ARG cc_start: 0.9200 (OUTLIER) cc_final: 0.8864 (ptm-80) REVERT: A 82 GLN cc_start: 0.9394 (tp40) cc_final: 0.9097 (mm-40) REVERT: A 98 GLU cc_start: 0.8805 (pt0) cc_final: 0.8534 (pt0) REVERT: A 104 LYS cc_start: 0.9551 (ttpp) cc_final: 0.9321 (mtmm) REVERT: A 105 GLN cc_start: 0.9545 (mm-40) cc_final: 0.9262 (mm-40) REVERT: A 172 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7839 (t80) REVERT: A 228 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9114 (mm) REVERT: A 231 GLN cc_start: 0.8133 (tm-30) cc_final: 0.7799 (tm-30) REVERT: A 269 TYR cc_start: 0.7776 (m-80) cc_final: 0.7531 (m-80) REVERT: A 294 ASP cc_start: 0.8803 (m-30) cc_final: 0.8503 (m-30) outliers start: 21 outliers final: 17 residues processed: 207 average time/residue: 0.1416 time to fit residues: 37.2895 Evaluate side-chains 214 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 194 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU 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 237 SER Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain A residue 79 ARG 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 228 LEU Chi-restraints excluded: chain A residue 264 ILE 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: 0.0470 chunk 44 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 34 optimal weight: 0.3980 chunk 51 optimal weight: 0.6980 chunk 47 optimal weight: 0.0570 chunk 41 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.3396 ------------------------------------------------------------------------------- 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: 0.7941 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4272 Z= 0.234 Angle : 0.860 13.083 5803 Z= 0.405 Chirality : 0.044 0.208 688 Planarity : 0.005 0.056 692 Dihedral : 5.861 59.464 611 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.72 % Allowed : 37.08 % Favored : 58.20 % 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: 2.50 (0.36), residues: 522 helix: 2.39 (0.25), residues: 400 sheet: None (None), residues: 0 loop : -0.90 (0.56), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 277 HIS 0.004 0.001 HIS B 151 PHE 0.025 0.001 PHE B 185 TYR 0.017 0.002 TYR B 57 ARG 0.009 0.001 ARG B 79 *********************** 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 226 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 205 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 GLN cc_start: 0.9354 (mm110) cc_final: 0.8972 (tp40) REVERT: B 101 ASP cc_start: 0.8852 (m-30) cc_final: 0.8509 (m-30) REVERT: B 104 LYS cc_start: 0.9528 (ttmm) cc_final: 0.9188 (mtmm) REVERT: B 231 GLN cc_start: 0.8602 (tt0) cc_final: 0.8221 (tt0) REVERT: A 79 ARG cc_start: 0.9203 (OUTLIER) cc_final: 0.8855 (ptm-80) REVERT: A 95 GLN cc_start: 0.8903 (mm110) cc_final: 0.8695 (mm110) REVERT: A 98 GLU cc_start: 0.8840 (pt0) cc_final: 0.8538 (pt0) REVERT: A 100 GLU cc_start: 0.9351 (mm-30) cc_final: 0.9055 (mm-30) REVERT: A 172 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.7826 (t80) REVERT: A 228 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9142 (mm) REVERT: A 231 GLN cc_start: 0.8119 (tm-30) cc_final: 0.7777 (tm-30) REVERT: A 269 TYR cc_start: 0.7781 (m-80) cc_final: 0.7533 (m-80) REVERT: A 294 ASP cc_start: 0.8803 (m-30) cc_final: 0.8487 (m-30) outliers start: 21 outliers final: 16 residues processed: 208 average time/residue: 0.1451 time to fit residues: 38.7114 Evaluate side-chains 221 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 202 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 148 VAL 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 278 ILE Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain A residue 79 ARG 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 228 LEU Chi-restraints excluded: chain A residue 278 ILE 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: 5.9990 chunk 32 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 0.0970 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7983 moved from start: 0.5256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 4272 Z= 0.280 Angle : 0.879 12.293 5803 Z= 0.418 Chirality : 0.044 0.213 688 Planarity : 0.005 0.059 692 Dihedral : 5.922 58.511 611 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.27 % Allowed : 37.53 % Favored : 58.20 % 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: 2.38 (0.36), residues: 522 helix: 2.29 (0.24), residues: 403 sheet: None (None), residues: 0 loop : -1.01 (0.58), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 277 HIS 0.003 0.001 HIS B 151 PHE 0.029 0.002 PHE A 158 TYR 0.014 0.002 TYR A 266 ARG 0.008 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 fitting. rotamer outliers: 19 poor density : 198 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 GLN cc_start: 0.9367 (mm110) cc_final: 0.8999 (tp40) REVERT: B 101 ASP cc_start: 0.8875 (m-30) cc_final: 0.8570 (m-30) REVERT: B 104 LYS cc_start: 0.9550 (ttmm) cc_final: 0.9219 (mtmm) REVERT: B 195 MET cc_start: 0.3364 (tpp) cc_final: 0.1828 (ttp) REVERT: B 231 GLN cc_start: 0.8630 (tt0) cc_final: 0.8227 (tt0) REVERT: A 95 GLN cc_start: 0.8877 (mm110) cc_final: 0.8599 (mm110) REVERT: A 98 GLU cc_start: 0.8875 (pt0) cc_final: 0.8506 (pt0) REVERT: A 172 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7847 (t80) REVERT: A 195 MET cc_start: 0.8850 (tmm) cc_final: 0.8614 (tpt) REVERT: A 228 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9169 (mm) REVERT: A 231 GLN cc_start: 0.8140 (tm-30) cc_final: 0.7798 (tm-30) REVERT: A 269 TYR cc_start: 0.7831 (m-80) cc_final: 0.7584 (m-80) outliers start: 19 outliers final: 14 residues processed: 202 average time/residue: 0.1318 time to fit residues: 34.2683 Evaluate side-chains 209 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 193 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 148 VAL 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 278 ILE Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 296 LEU 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 228 LEU Chi-restraints excluded: chain A residue 278 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 0.3980 chunk 7 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 31 optimal weight: 0.0170 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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 = 0.4028 r_free = 0.4028 target = 0.154302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.103931 restraints weight = 7352.774| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 4.15 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.5383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 4272 Z= 0.253 Angle : 0.894 12.135 5803 Z= 0.423 Chirality : 0.044 0.221 688 Planarity : 0.005 0.055 692 Dihedral : 5.750 59.878 611 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.82 % Allowed : 38.43 % Favored : 57.75 % 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: 2.24 (0.25), residues: 403 sheet: None (None), residues: 0 loop : -0.99 (0.59), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 277 HIS 0.004 0.001 HIS B 151 PHE 0.027 0.001 PHE A 158 TYR 0.017 0.002 TYR B 57 ARG 0.009 0.001 ARG B 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1327.14 seconds wall clock time: 25 minutes 27.19 seconds (1527.19 seconds total)