Starting phenix.real_space_refine on Sat May 10 00:02:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8de7_27386/05_2025/8de7_27386.cif Found real_map, /net/cci-nas-00/data/ceres_data/8de7_27386/05_2025/8de7_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_27386/05_2025/8de7_27386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8de7_27386/05_2025/8de7_27386.map" model { file = "/net/cci-nas-00/data/ceres_data/8de7_27386/05_2025/8de7_27386.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8de7_27386/05_2025/8de7_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-5687/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: 3.14, per 1000 atoms: 0.75 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: 1.14 Conformation dependent library (CDL) restraints added in 459.4 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: 0.36 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: 1.11 Time building geometry restraints manager: 1.26 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.890 Find NCS groups from input model: 0.160 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.850 ------------------------------------------------------------------------------- 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 4273 Z= 0.302 Angle : 1.055 12.541 5805 Z= 0.578 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 Details of bonding type rmsd hydrogen bonds : bond 0.08583 ( 334) hydrogen bonds : angle 4.65791 ( 1002) SS BOND : bond 0.00150 ( 1) SS BOND : angle 5.25403 ( 2) covalent geometry : bond 0.00636 ( 4272) covalent geometry : angle 1.05109 ( 5803) *********************** 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 : 0.465 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: 0.1546 time to fit residues: 48.3661 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 : 0.648 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.154635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.103373 restraints weight = 7206.868| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 4.32 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 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 4273 Z= 0.184 Angle : 0.772 12.217 5805 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 Details of bonding type rmsd hydrogen bonds : bond 0.04611 ( 334) hydrogen bonds : angle 4.21032 ( 1002) SS BOND : bond 0.00196 ( 1) SS BOND : angle 1.77570 ( 2) covalent geometry : bond 0.00433 ( 4272) covalent geometry : angle 0.77128 ( 5803) *********************** 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 : 0.418 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: 0.8570 (tt0) cc_final: 0.8270 (tt0) REVERT: B 82 GLN cc_start: 0.9513 (mm110) cc_final: 0.9193 (mm-40) REVERT: B 83 GLU cc_start: 0.9121 (tm-30) cc_final: 0.8809 (mp0) REVERT: B 98 GLU cc_start: 0.9519 (mp0) cc_final: 0.9284 (mp0) REVERT: B 101 ASP cc_start: 0.9632 (t0) cc_final: 0.9266 (m-30) REVERT: B 104 LYS cc_start: 0.9434 (ttmm) cc_final: 0.9165 (mtmm) REVERT: B 231 GLN cc_start: 0.9113 (tt0) cc_final: 0.8483 (tt0) REVERT: B 269 TYR cc_start: 0.8215 (m-80) cc_final: 0.7951 (m-80) REVERT: A 42 MET cc_start: 0.8440 (mmm) cc_final: 0.8211 (mmm) REVERT: A 48 LEU cc_start: 0.9473 (tp) cc_final: 0.9233 (tp) REVERT: A 52 LEU cc_start: 0.9530 (mt) cc_final: 0.9309 (mt) REVERT: A 56 LEU cc_start: 0.9625 (tp) cc_final: 0.9405 (tp) REVERT: A 104 LYS cc_start: 0.9569 (ttpp) cc_final: 0.9286 (mtmm) REVERT: A 216 LEU cc_start: 0.9467 (mp) cc_final: 0.9256 (mp) REVERT: A 269 TYR cc_start: 0.8441 (m-80) cc_final: 0.7973 (m-80) outliers start: 17 outliers final: 8 residues processed: 221 average time/residue: 0.1395 time to fit residues: 39.1798 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 : 0.470 ------------------------------------------------------------------------------- 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 41 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 31 optimal weight: 0.4980 chunk 43 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.150827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.103087 restraints weight = 7146.137| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 3.94 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 4273 Z= 0.197 Angle : 0.746 10.803 5805 Z= 0.375 Chirality : 0.045 0.298 688 Planarity : 0.005 0.060 692 Dihedral : 7.664 49.478 611 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.82 % Allowed : 23.37 % Favored : 72.81 % 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: 3.40 (0.35), residues: 522 helix: 3.01 (0.23), residues: 407 sheet: None (None), residues: 0 loop : -0.76 (0.55), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 277 HIS 0.004 0.001 HIS A 232 PHE 0.020 0.002 PHE A 158 TYR 0.018 0.002 TYR A 266 ARG 0.004 0.001 ARG B 79 Details of bonding type rmsd hydrogen bonds : bond 0.04238 ( 334) hydrogen bonds : angle 4.15373 ( 1002) SS BOND : bond 0.00133 ( 1) SS BOND : angle 1.63004 ( 2) covalent geometry : bond 0.00478 ( 4272) covalent geometry : angle 0.74515 ( 5803) *********************** 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 224 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 207 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 GLN cc_start: 0.9494 (mm110) cc_final: 0.9127 (mm-40) REVERT: B 101 ASP cc_start: 0.9639 (t0) cc_final: 0.9309 (m-30) REVERT: B 104 LYS cc_start: 0.9437 (ttmm) cc_final: 0.9182 (mtmm) REVERT: B 207 ARG cc_start: 0.8442 (ptm160) cc_final: 0.8224 (ptm160) REVERT: B 231 GLN cc_start: 0.9002 (tt0) cc_final: 0.8271 (tt0) REVERT: B 269 TYR cc_start: 0.8173 (m-80) cc_final: 0.7916 (m-80) REVERT: A 42 MET cc_start: 0.8507 (mmm) cc_final: 0.8203 (mmm) REVERT: A 48 LEU cc_start: 0.9486 (tp) cc_final: 0.9244 (tp) REVERT: A 51 PHE cc_start: 0.9169 (t80) cc_final: 0.8963 (t80) REVERT: A 52 LEU cc_start: 0.9556 (mt) cc_final: 0.9347 (mt) REVERT: A 56 LEU cc_start: 0.9631 (tp) cc_final: 0.9420 (tp) REVERT: A 99 LEU cc_start: 0.9452 (pp) cc_final: 0.8919 (pp) REVERT: A 100 GLU cc_start: 0.9423 (mm-30) cc_final: 0.9157 (mm-30) REVERT: A 104 LYS cc_start: 0.9551 (ttpp) cc_final: 0.9251 (mtmm) REVERT: A 122 GLN cc_start: 0.8750 (pm20) cc_final: 0.8446 (pm20) REVERT: A 228 LEU cc_start: 0.9553 (mm) cc_final: 0.9347 (mm) REVERT: A 240 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8379 (mt-10) REVERT: A 269 TYR cc_start: 0.8410 (m-80) cc_final: 0.7966 (m-80) REVERT: A 270 TYR cc_start: 0.8205 (t80) cc_final: 0.7935 (t80) outliers start: 17 outliers final: 10 residues processed: 212 average time/residue: 0.1260 time to fit residues: 34.0614 Evaluate side-chains 210 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 200 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 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 148 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 8 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 5 optimal weight: 0.0270 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 1 optimal weight: 0.5980 chunk 21 optimal weight: 0.0000 chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 overall best weight: 0.3842 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.153767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.106080 restraints weight = 7225.055| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 3.92 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4273 Z= 0.155 Angle : 0.752 9.268 5805 Z= 0.368 Chirality : 0.044 0.276 688 Planarity : 0.005 0.065 692 Dihedral : 6.200 41.412 611 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.27 % Allowed : 25.17 % Favored : 70.56 % 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: 3.08 (0.36), residues: 522 helix: 2.81 (0.24), residues: 410 sheet: None (None), residues: 0 loop : -1.09 (0.58), 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 0.037 0.002 PHE A 196 TYR 0.013 0.002 TYR A 266 ARG 0.005 0.001 ARG B 79 Details of bonding type rmsd hydrogen bonds : bond 0.04022 ( 334) hydrogen bonds : angle 4.14317 ( 1002) SS BOND : bond 0.00022 ( 1) SS BOND : angle 1.17354 ( 2) covalent geometry : bond 0.00353 ( 4272) covalent geometry : angle 0.75186 ( 5803) *********************** 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 230 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 211 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9165 (mp) REVERT: B 82 GLN cc_start: 0.9498 (mm110) cc_final: 0.9194 (mm-40) REVERT: B 95 GLN cc_start: 0.9173 (mp10) cc_final: 0.8872 (mp10) REVERT: B 98 GLU cc_start: 0.9409 (mp0) cc_final: 0.9145 (mp0) REVERT: B 104 LYS cc_start: 0.9460 (ttmm) cc_final: 0.9200 (mtmm) REVERT: B 195 MET cc_start: 0.4691 (ttp) cc_final: 0.4422 (tpp) REVERT: B 231 GLN cc_start: 0.8979 (tt0) cc_final: 0.8260 (tt0) REVERT: B 240 GLU cc_start: 0.8465 (mt-10) cc_final: 0.7916 (pt0) REVERT: B 270 TYR cc_start: 0.8373 (t80) cc_final: 0.8039 (t80) REVERT: B 289 LEU cc_start: 0.8709 (mp) cc_final: 0.8464 (mp) REVERT: A 42 MET cc_start: 0.8440 (mmm) cc_final: 0.8168 (mmm) REVERT: A 48 LEU cc_start: 0.9472 (tp) cc_final: 0.9231 (tp) REVERT: A 51 PHE cc_start: 0.9153 (t80) cc_final: 0.8928 (t80) REVERT: A 52 LEU cc_start: 0.9547 (mt) cc_final: 0.9342 (mt) REVERT: A 56 LEU cc_start: 0.9610 (tp) cc_final: 0.9409 (tp) REVERT: A 104 LYS cc_start: 0.9548 (ttpp) cc_final: 0.9283 (mtmm) REVERT: A 122 GLN cc_start: 0.8799 (pm20) cc_final: 0.8497 (pm20) REVERT: A 151 HIS cc_start: 0.8509 (m90) cc_final: 0.7934 (m-70) REVERT: A 240 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8360 (mt-10) REVERT: A 263 GLU cc_start: 0.8414 (pp20) cc_final: 0.8179 (pp20) REVERT: A 268 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7473 (p0) REVERT: A 269 TYR cc_start: 0.8454 (m-80) cc_final: 0.7883 (m-80) outliers start: 19 outliers final: 11 residues processed: 214 average time/residue: 0.1305 time to fit residues: 35.6052 Evaluate side-chains 218 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 205 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 258 VAL 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 268 ASP Chi-restraints excluded: chain A residue 278 ILE 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 20 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 41 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.149020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.097919 restraints weight = 7472.637| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 4.26 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 4273 Z= 0.202 Angle : 0.771 11.901 5805 Z= 0.384 Chirality : 0.044 0.242 688 Planarity : 0.005 0.068 692 Dihedral : 6.041 41.257 611 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.72 % Allowed : 28.31 % Favored : 66.97 % 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: 2.78 (0.36), residues: 522 helix: 2.57 (0.24), residues: 410 sheet: None (None), residues: 0 loop : -1.08 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 277 HIS 0.004 0.001 HIS A 91 PHE 0.019 0.002 PHE B 158 TYR 0.012 0.002 TYR A 270 ARG 0.006 0.001 ARG A 297 Details of bonding type rmsd hydrogen bonds : bond 0.04103 ( 334) hydrogen bonds : angle 4.25749 ( 1002) SS BOND : bond 0.00213 ( 1) SS BOND : angle 1.31734 ( 2) covalent geometry : bond 0.00495 ( 4272) covalent geometry : angle 0.77040 ( 5803) *********************** 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 225 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 GLN cc_start: 0.9512 (mm110) cc_final: 0.9156 (mm-40) REVERT: B 101 ASP cc_start: 0.9650 (t70) cc_final: 0.9322 (m-30) REVERT: B 104 LYS cc_start: 0.9463 (ttmm) cc_final: 0.9210 (mtmm) REVERT: B 231 GLN cc_start: 0.8945 (tt0) cc_final: 0.8198 (tt0) REVERT: B 270 TYR cc_start: 0.8420 (t80) cc_final: 0.8082 (t80) REVERT: A 42 MET cc_start: 0.8518 (mmm) cc_final: 0.8281 (mmm) REVERT: A 48 LEU cc_start: 0.9485 (tp) cc_final: 0.9243 (tp) REVERT: A 51 PHE cc_start: 0.9174 (t80) cc_final: 0.8974 (t80) REVERT: A 52 LEU cc_start: 0.9568 (mt) cc_final: 0.9337 (mt) REVERT: A 56 LEU cc_start: 0.9625 (tp) cc_final: 0.9420 (tp) REVERT: A 99 LEU cc_start: 0.9442 (pp) cc_final: 0.8966 (pp) REVERT: A 104 LYS cc_start: 0.9553 (ttpp) cc_final: 0.9232 (mtmm) REVERT: A 115 ASN cc_start: 0.8746 (t0) cc_final: 0.8509 (t0) REVERT: A 122 GLN cc_start: 0.8854 (pm20) cc_final: 0.8462 (pm20) REVERT: A 151 HIS cc_start: 0.8568 (m90) cc_final: 0.7861 (m90) REVERT: A 240 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8395 (mt-10) REVERT: A 263 GLU cc_start: 0.8634 (pp20) cc_final: 0.8411 (pp20) REVERT: A 268 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7558 (p0) REVERT: A 269 TYR cc_start: 0.8448 (m-80) cc_final: 0.7823 (m-80) outliers start: 21 outliers final: 15 residues processed: 209 average time/residue: 0.1296 time to fit residues: 34.5629 Evaluate side-chains 214 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 198 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 214 PHE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 258 VAL 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 268 ASP Chi-restraints excluded: chain A residue 278 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 3 optimal weight: 0.9990 chunk 5 optimal weight: 0.0070 chunk 38 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.151967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.100847 restraints weight = 7275.765| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 4.24 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 4273 Z= 0.170 Angle : 0.796 11.901 5805 Z= 0.386 Chirality : 0.043 0.197 688 Planarity : 0.005 0.065 692 Dihedral : 5.913 45.394 611 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.49 % Allowed : 31.24 % Favored : 64.27 % 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: 2.63 (0.36), residues: 522 helix: 2.47 (0.24), residues: 410 sheet: None (None), residues: 0 loop : -1.15 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 44 HIS 0.007 0.001 HIS A 91 PHE 0.018 0.001 PHE B 158 TYR 0.014 0.002 TYR B 57 ARG 0.006 0.001 ARG B 79 Details of bonding type rmsd hydrogen bonds : bond 0.04043 ( 334) hydrogen bonds : angle 4.30457 ( 1002) SS BOND : bond 0.00122 ( 1) SS BOND : angle 1.33889 ( 2) covalent geometry : bond 0.00409 ( 4272) covalent geometry : angle 0.79537 ( 5803) *********************** 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 227 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 207 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 GLN cc_start: 0.9512 (mm110) cc_final: 0.9127 (tp40) REVERT: B 101 ASP cc_start: 0.9654 (t70) cc_final: 0.9328 (m-30) REVERT: B 104 LYS cc_start: 0.9450 (ttmm) cc_final: 0.9205 (mtmm) REVERT: B 195 MET cc_start: 0.3640 (tpp) cc_final: 0.2384 (ttp) REVERT: B 231 GLN cc_start: 0.8927 (tt0) cc_final: 0.8175 (tt0) REVERT: B 240 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8192 (pt0) REVERT: B 270 TYR cc_start: 0.8417 (t80) cc_final: 0.8146 (t80) REVERT: A 42 MET cc_start: 0.8524 (mmm) cc_final: 0.8319 (mmm) REVERT: A 48 LEU cc_start: 0.9471 (tp) cc_final: 0.9222 (tp) REVERT: A 52 LEU cc_start: 0.9556 (mt) cc_final: 0.9328 (mt) REVERT: A 100 GLU cc_start: 0.9442 (mm-30) cc_final: 0.9218 (mm-30) REVERT: A 104 LYS cc_start: 0.9525 (ttpp) cc_final: 0.9246 (mtmm) REVERT: A 115 ASN cc_start: 0.8723 (t0) cc_final: 0.8446 (t0) REVERT: A 122 GLN cc_start: 0.8845 (pm20) cc_final: 0.8469 (pm20) REVERT: A 151 HIS cc_start: 0.8562 (m90) cc_final: 0.8046 (m170) REVERT: A 172 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.8359 (t80) REVERT: A 240 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8359 (mt-10) REVERT: A 263 GLU cc_start: 0.8705 (pp20) cc_final: 0.8459 (pp20) REVERT: A 268 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7551 (p0) REVERT: A 269 TYR cc_start: 0.8459 (m-80) cc_final: 0.7816 (m-80) outliers start: 20 outliers final: 14 residues processed: 212 average time/residue: 0.1336 time to fit residues: 36.2260 Evaluate side-chains 218 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 202 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU 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 258 VAL Chi-restraints excluded: chain B residue 263 GLU 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 268 ASP 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 24 optimal weight: 0.7980 chunk 8 optimal weight: 0.0170 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 0.0050 chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 overall best weight: 0.4032 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.153253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.101989 restraints weight = 7223.694| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 4.20 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4273 Z= 0.162 Angle : 0.833 13.700 5805 Z= 0.402 Chirality : 0.044 0.239 688 Planarity : 0.005 0.062 692 Dihedral : 5.947 50.138 611 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.82 % Allowed : 34.16 % Favored : 62.02 % 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: 2.44 (0.36), residues: 522 helix: 2.31 (0.24), residues: 410 sheet: None (None), residues: 0 loop : -1.12 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 44 HIS 0.003 0.001 HIS A 91 PHE 0.026 0.001 PHE A 51 TYR 0.011 0.002 TYR A 270 ARG 0.006 0.001 ARG A 297 Details of bonding type rmsd hydrogen bonds : bond 0.03991 ( 334) hydrogen bonds : angle 4.33758 ( 1002) SS BOND : bond 0.00084 ( 1) SS BOND : angle 1.20815 ( 2) covalent geometry : bond 0.00377 ( 4272) covalent geometry : angle 0.83249 ( 5803) *********************** 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 226 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 209 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 GLN cc_start: 0.9500 (mm110) cc_final: 0.9105 (tp40) REVERT: B 101 ASP cc_start: 0.9657 (t70) cc_final: 0.9248 (m-30) REVERT: B 104 LYS cc_start: 0.9433 (ttmm) cc_final: 0.9142 (mtmm) REVERT: B 195 MET cc_start: 0.3833 (tpp) cc_final: 0.2552 (ttp) REVERT: B 231 GLN cc_start: 0.8919 (tt0) cc_final: 0.8180 (tt0) REVERT: B 240 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8060 (pt0) REVERT: B 270 TYR cc_start: 0.8391 (t80) cc_final: 0.8127 (t80) REVERT: A 48 LEU cc_start: 0.9463 (tp) cc_final: 0.9221 (tp) REVERT: A 52 LEU cc_start: 0.9558 (mt) cc_final: 0.9315 (mt) REVERT: A 100 GLU cc_start: 0.9401 (mm-30) cc_final: 0.8985 (mm-30) REVERT: A 104 LYS cc_start: 0.9515 (ttpp) cc_final: 0.9223 (mtmm) REVERT: A 115 ASN cc_start: 0.8760 (t0) cc_final: 0.8463 (t0) REVERT: A 122 GLN cc_start: 0.8884 (pm20) cc_final: 0.8533 (pm20) REVERT: A 151 HIS cc_start: 0.8570 (m90) cc_final: 0.7806 (m90) REVERT: A 172 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.8389 (t80) REVERT: A 240 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8338 (mt-10) REVERT: A 263 GLU cc_start: 0.8759 (pp20) cc_final: 0.8515 (pp20) REVERT: A 268 ASP cc_start: 0.7783 (OUTLIER) cc_final: 0.7514 (p0) REVERT: A 269 TYR cc_start: 0.8464 (m-80) cc_final: 0.7823 (m-80) outliers start: 17 outliers final: 14 residues processed: 211 average time/residue: 0.1326 time to fit residues: 35.7032 Evaluate side-chains 215 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 199 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 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 172 PHE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 268 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 6 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 10 optimal weight: 0.0070 chunk 35 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 45 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.151530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.102685 restraints weight = 7260.949| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 4.13 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4273 Z= 0.176 Angle : 0.872 13.697 5805 Z= 0.422 Chirality : 0.046 0.329 688 Planarity : 0.005 0.064 692 Dihedral : 5.894 50.773 611 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.04 % Allowed : 35.28 % Favored : 60.67 % 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: 2.33 (0.36), residues: 522 helix: 2.22 (0.24), residues: 410 sheet: None (None), residues: 0 loop : -1.09 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 127 HIS 0.005 0.001 HIS A 91 PHE 0.052 0.002 PHE A 196 TYR 0.014 0.002 TYR B 57 ARG 0.008 0.001 ARG B 79 Details of bonding type rmsd hydrogen bonds : bond 0.04030 ( 334) hydrogen bonds : angle 4.43830 ( 1002) SS BOND : bond 0.00091 ( 1) SS BOND : angle 0.80789 ( 2) covalent geometry : bond 0.00420 ( 4272) covalent geometry : angle 0.87245 ( 5803) *********************** 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 216 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 198 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ARG cc_start: 0.9181 (mtp-110) cc_final: 0.8932 (ttp-110) REVERT: B 82 GLN cc_start: 0.9470 (mm110) cc_final: 0.9046 (tp40) REVERT: B 99 LEU cc_start: 0.9705 (tp) cc_final: 0.9449 (mt) REVERT: B 104 LYS cc_start: 0.9494 (ttmm) cc_final: 0.9212 (mtmm) REVERT: B 126 MET cc_start: 0.8901 (tpt) cc_final: 0.8696 (tpt) REVERT: B 240 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8064 (pt0) REVERT: A 42 MET cc_start: 0.8473 (mmm) cc_final: 0.8227 (mmp) REVERT: A 48 LEU cc_start: 0.9492 (tp) cc_final: 0.9284 (tp) REVERT: A 52 LEU cc_start: 0.9563 (mt) cc_final: 0.9293 (mt) REVERT: A 100 GLU cc_start: 0.9403 (mm-30) cc_final: 0.9095 (mm-30) REVERT: A 115 ASN cc_start: 0.8779 (t0) cc_final: 0.8481 (t0) REVERT: A 122 GLN cc_start: 0.8920 (pm20) cc_final: 0.8539 (pm20) REVERT: A 151 HIS cc_start: 0.8604 (m90) cc_final: 0.8131 (m170) REVERT: A 172 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.8391 (t80) REVERT: A 240 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8321 (mt-10) REVERT: A 263 GLU cc_start: 0.8779 (pp20) cc_final: 0.8519 (pp20) REVERT: A 268 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7502 (p0) REVERT: A 269 TYR cc_start: 0.8504 (m-80) cc_final: 0.7781 (m-80) outliers start: 18 outliers final: 14 residues processed: 200 average time/residue: 0.1332 time to fit residues: 34.0924 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 : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 278 ILE Chi-restraints excluded: chain B residue 279 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 268 ASP 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 7 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 38 optimal weight: 0.4980 chunk 42 optimal weight: 30.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3947 r_free = 0.3947 target = 0.148959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.101364 restraints weight = 7131.316| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.87 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4273 Z= 0.182 Angle : 0.911 13.611 5805 Z= 0.440 Chirality : 0.046 0.338 688 Planarity : 0.005 0.065 692 Dihedral : 5.977 51.425 611 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.04 % Allowed : 35.96 % Favored : 60.00 % 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: 2.21 (0.36), residues: 522 helix: 2.12 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -1.02 (0.58), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 127 HIS 0.004 0.001 HIS A 91 PHE 0.026 0.001 PHE A 51 TYR 0.023 0.002 TYR B 270 ARG 0.006 0.001 ARG B 79 Details of bonding type rmsd hydrogen bonds : bond 0.04059 ( 334) hydrogen bonds : angle 4.42290 ( 1002) SS BOND : bond 0.00880 ( 1) SS BOND : angle 0.18942 ( 2) covalent geometry : bond 0.00432 ( 4272) covalent geometry : angle 0.91069 ( 5803) *********************** 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 216 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 198 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ARG cc_start: 0.9181 (mtp-110) cc_final: 0.8888 (ttp-110) REVERT: B 82 GLN cc_start: 0.9479 (mm110) cc_final: 0.9060 (tp40) REVERT: B 99 LEU cc_start: 0.9698 (tp) cc_final: 0.9449 (mt) REVERT: B 104 LYS cc_start: 0.9512 (ttmm) cc_final: 0.9231 (mtmm) REVERT: B 126 MET cc_start: 0.8987 (tpt) cc_final: 0.8752 (tpt) REVERT: B 231 GLN cc_start: 0.8822 (tt0) cc_final: 0.8034 (tt0) REVERT: B 240 GLU cc_start: 0.8473 (mt-10) cc_final: 0.7962 (pt0) REVERT: A 42 MET cc_start: 0.8496 (mmm) cc_final: 0.8295 (mmp) REVERT: A 48 LEU cc_start: 0.9488 (tp) cc_final: 0.9276 (tp) REVERT: A 52 LEU cc_start: 0.9558 (mt) cc_final: 0.9285 (mt) REVERT: A 79 ARG cc_start: 0.9369 (ttm-80) cc_final: 0.9155 (ptm160) REVERT: A 82 GLN cc_start: 0.9569 (tp40) cc_final: 0.9176 (mm-40) REVERT: A 100 GLU cc_start: 0.9427 (mm-30) cc_final: 0.8956 (mm-30) REVERT: A 115 ASN cc_start: 0.8819 (t0) cc_final: 0.8519 (t0) REVERT: A 122 GLN cc_start: 0.8926 (pm20) cc_final: 0.8548 (pm20) REVERT: A 151 HIS cc_start: 0.8614 (m90) cc_final: 0.8130 (m170) REVERT: A 172 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8347 (t80) REVERT: A 240 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8331 (mt-10) REVERT: A 263 GLU cc_start: 0.8707 (pp20) cc_final: 0.8435 (pp20) REVERT: A 268 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7462 (p0) REVERT: A 269 TYR cc_start: 0.8469 (m-80) cc_final: 0.7724 (m-80) outliers start: 18 outliers final: 16 residues processed: 200 average time/residue: 0.1347 time to fit residues: 34.3193 Evaluate side-chains 214 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 196 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 278 ILE Chi-restraints excluded: chain B residue 279 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 264 ILE Chi-restraints excluded: chain A residue 268 ASP 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 20 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 19 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 39 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 chunk 49 optimal weight: 0.2980 chunk 23 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.150366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.103423 restraints weight = 7229.854| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.92 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4273 Z= 0.173 Angle : 0.924 13.836 5805 Z= 0.442 Chirality : 0.047 0.351 688 Planarity : 0.005 0.064 692 Dihedral : 5.819 55.888 611 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.82 % Allowed : 36.63 % 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: 2.19 (0.36), residues: 522 helix: 2.14 (0.24), residues: 405 sheet: None (None), residues: 0 loop : -1.06 (0.57), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 127 HIS 0.003 0.001 HIS A 151 PHE 0.056 0.002 PHE A 196 TYR 0.025 0.002 TYR B 270 ARG 0.006 0.001 ARG B 79 Details of bonding type rmsd hydrogen bonds : bond 0.03982 ( 334) hydrogen bonds : angle 4.46303 ( 1002) SS BOND : bond 0.00607 ( 1) SS BOND : angle 0.03671 ( 2) covalent geometry : bond 0.00409 ( 4272) covalent geometry : angle 0.92411 ( 5803) ********************** 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 215 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 198 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ARG cc_start: 0.9163 (mtp-110) cc_final: 0.8848 (ttp-110) REVERT: B 82 GLN cc_start: 0.9485 (mm110) cc_final: 0.9089 (tp40) REVERT: B 99 LEU cc_start: 0.9692 (tp) cc_final: 0.9453 (mt) REVERT: B 104 LYS cc_start: 0.9518 (ttmm) cc_final: 0.9246 (mtmm) REVERT: B 126 MET cc_start: 0.8938 (tpt) cc_final: 0.8662 (tpt) REVERT: B 231 GLN cc_start: 0.8798 (tt0) cc_final: 0.7976 (tt0) REVERT: B 240 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8039 (pt0) REVERT: A 42 MET cc_start: 0.8514 (mmm) cc_final: 0.8206 (mmp) REVERT: A 48 LEU cc_start: 0.9490 (tp) cc_final: 0.9275 (tp) REVERT: A 52 LEU cc_start: 0.9548 (mt) cc_final: 0.9264 (mt) REVERT: A 90 MET cc_start: 0.9171 (tmm) cc_final: 0.8770 (ppp) REVERT: A 100 GLU cc_start: 0.9432 (mm-30) cc_final: 0.8957 (mm-30) REVERT: A 115 ASN cc_start: 0.8815 (t0) cc_final: 0.8518 (t0) REVERT: A 122 GLN cc_start: 0.8952 (pm20) cc_final: 0.8566 (pm20) REVERT: A 151 HIS cc_start: 0.8621 (m90) cc_final: 0.8147 (m170) REVERT: A 172 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.8306 (t80) REVERT: A 240 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8313 (mt-10) REVERT: A 263 GLU cc_start: 0.8720 (pp20) cc_final: 0.8414 (pp20) REVERT: A 268 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7441 (p0) REVERT: A 269 TYR cc_start: 0.8484 (m-80) cc_final: 0.7738 (m-80) outliers start: 17 outliers final: 15 residues processed: 201 average time/residue: 0.1338 time to fit residues: 34.5749 Evaluate side-chains 211 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 194 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 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 278 ILE Chi-restraints excluded: chain B residue 279 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 268 ASP 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 46 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 15 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3962 r_free = 0.3962 target = 0.149332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.099883 restraints weight = 7384.976| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 4.22 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.5277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4273 Z= 0.179 Angle : 0.929 13.640 5805 Z= 0.444 Chirality : 0.047 0.350 688 Planarity : 0.005 0.062 692 Dihedral : 5.806 56.184 611 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.04 % Allowed : 35.73 % Favored : 60.22 % 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: 2.08 (0.36), residues: 522 helix: 2.06 (0.24), residues: 406 sheet: None (None), residues: 0 loop : -1.09 (0.58), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 127 HIS 0.003 0.001 HIS B 151 PHE 0.027 0.001 PHE A 51 TYR 0.012 0.002 TYR A 270 ARG 0.006 0.001 ARG A 297 Details of bonding type rmsd hydrogen bonds : bond 0.04032 ( 334) hydrogen bonds : angle 4.48771 ( 1002) SS BOND : bond 0.00411 ( 1) SS BOND : angle 0.09511 ( 2) covalent geometry : bond 0.00427 ( 4272) covalent geometry : angle 0.92899 ( 5803) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2179.56 seconds wall clock time: 38 minutes 30.89 seconds (2310.89 seconds total)