Starting phenix.real_space_refine on Thu Mar 6 01:05:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8de7_27386/03_2025/8de7_27386.cif Found real_map, /net/cci-nas-00/data/ceres_data/8de7_27386/03_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_27386/03_2025/8de7_27386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8de7_27386/03_2025/8de7_27386.map" model { file = "/net/cci-nas-00/data/ceres_data/8de7_27386/03_2025/8de7_27386.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8de7_27386/03_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.06, per 1000 atoms: 0.73 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: 1.08 Conformation dependent library (CDL) restraints added in 554.8 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: 0.32 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: 1.10 Time building geometry restraints manager: 1.27 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: 0.690 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.150 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 4272 Z= 0.388 Angle : 1.051 12.541 5803 Z= 0.576 Chirality : 0.058 0.258 688 Planarity : 0.008 0.069 692 Dihedral : 16.507 98.164 1519 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.90 % Allowed : 0.22 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.08 (0.33), residues: 522 helix: 3.44 (0.22), residues: 402 sheet: None (None), residues: 0 loop : -0.10 (0.51), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 199 HIS 0.006 0.002 HIS B 151 PHE 0.023 0.003 PHE A 285 TYR 0.017 0.003 TYR B 266 ARG 0.005 0.001 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 251 time to evaluate : 0.461 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: 0.1571 time to fit residues: 48.9920 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 : 0.475 ------------------------------------------------------------------------------- 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 = 0.154437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.103870 restraints weight = 7209.381| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 4.32 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4272 Z= 0.274 Angle : 0.771 12.217 5803 Z= 0.381 Chirality : 0.046 0.285 688 Planarity : 0.005 0.048 692 Dihedral : 9.241 59.133 612 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 3.82 % Allowed : 19.78 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.77 (0.35), residues: 522 helix: 3.22 (0.23), residues: 408 sheet: None (None), residues: 0 loop : -0.43 (0.55), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 277 HIS 0.005 0.001 HIS B 151 PHE 0.019 0.002 PHE A 244 TYR 0.015 0.002 TYR B 162 ARG 0.003 0.001 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 218 time to evaluate : 0.789 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: 0.8561 (tt0) cc_final: 0.8261 (tt0) REVERT: B 82 GLN cc_start: 0.9507 (mm110) cc_final: 0.9187 (mm-40) REVERT: B 83 GLU cc_start: 0.9109 (tm-30) cc_final: 0.8807 (mp0) REVERT: B 98 GLU cc_start: 0.9515 (mp0) cc_final: 0.9279 (mp0) REVERT: B 101 ASP cc_start: 0.9630 (t0) cc_final: 0.9266 (m-30) REVERT: B 104 LYS cc_start: 0.9436 (ttmm) cc_final: 0.9167 (mtmm) REVERT: B 231 GLN cc_start: 0.9114 (tt0) cc_final: 0.8483 (tt0) REVERT: B 269 TYR cc_start: 0.8213 (m-80) cc_final: 0.7948 (m-80) REVERT: A 42 MET cc_start: 0.8442 (mmm) cc_final: 0.8212 (mmm) REVERT: A 48 LEU cc_start: 0.9473 (tp) cc_final: 0.9234 (tp) REVERT: A 52 LEU cc_start: 0.9530 (mt) cc_final: 0.9308 (mt) REVERT: A 56 LEU cc_start: 0.9627 (tp) cc_final: 0.9407 (tp) REVERT: A 104 LYS cc_start: 0.9569 (ttpp) cc_final: 0.9286 (mtmm) REVERT: A 216 LEU cc_start: 0.9466 (mp) cc_final: 0.9254 (mp) REVERT: A 269 TYR cc_start: 0.8434 (m-80) cc_final: 0.7968 (m-80) outliers start: 17 outliers final: 8 residues processed: 221 average time/residue: 0.1462 time to fit residues: 40.9077 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: 5.9990 chunk 34 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 22 optimal weight: 0.0040 chunk 20 optimal weight: 0.7980 chunk 6 optimal weight: 0.0970 chunk 25 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 ASN A 232 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.151888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.105500 restraints weight = 7178.001| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 3.99 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 4272 Z= 0.241 Angle : 0.740 10.923 5803 Z= 0.369 Chirality : 0.044 0.286 688 Planarity : 0.005 0.058 692 Dihedral : 7.396 49.144 611 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.15 % Allowed : 22.70 % Favored : 74.16 % 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: 3.39 (0.35), residues: 522 helix: 3.01 (0.23), residues: 407 sheet: None (None), residues: 0 loop : -0.77 (0.55), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 277 HIS 0.006 0.001 HIS A 232 PHE 0.019 0.001 PHE A 158 TYR 0.018 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 222 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 208 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 GLN cc_start: 0.9485 (mm110) cc_final: 0.9112 (mm-40) REVERT: B 101 ASP cc_start: 0.9640 (t0) cc_final: 0.9315 (m-30) REVERT: B 104 LYS cc_start: 0.9425 (ttmm) cc_final: 0.9153 (mtmm) REVERT: B 231 GLN cc_start: 0.9007 (tt0) cc_final: 0.8270 (tt0) REVERT: B 269 TYR cc_start: 0.8163 (m-80) cc_final: 0.7940 (m-80) REVERT: B 289 LEU cc_start: 0.8705 (mp) cc_final: 0.8487 (mp) REVERT: A 42 MET cc_start: 0.8504 (mmm) cc_final: 0.8190 (mmm) REVERT: A 48 LEU cc_start: 0.9490 (tp) cc_final: 0.9264 (tp) REVERT: A 52 LEU cc_start: 0.9546 (mt) cc_final: 0.9328 (mt) REVERT: A 56 LEU cc_start: 0.9613 (tp) cc_final: 0.9402 (tp) REVERT: A 98 GLU cc_start: 0.9062 (pt0) cc_final: 0.8838 (pt0) REVERT: A 99 LEU cc_start: 0.9455 (pp) cc_final: 0.8920 (pp) REVERT: A 100 GLU cc_start: 0.9415 (mm-30) cc_final: 0.9205 (mm-30) REVERT: A 104 LYS cc_start: 0.9545 (ttpp) cc_final: 0.9269 (mtmm) REVERT: A 122 GLN cc_start: 0.8743 (pm20) cc_final: 0.8451 (pm20) REVERT: A 228 LEU cc_start: 0.9534 (mm) cc_final: 0.9324 (mm) REVERT: A 269 TYR cc_start: 0.8387 (m-80) cc_final: 0.7944 (m-80) outliers start: 14 outliers final: 8 residues processed: 213 average time/residue: 0.1350 time to fit residues: 36.7715 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 : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 8 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.151028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.100450 restraints weight = 7263.653| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 4.15 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 4272 Z= 0.267 Angle : 0.744 8.780 5803 Z= 0.368 Chirality : 0.044 0.264 688 Planarity : 0.005 0.067 692 Dihedral : 6.243 41.478 611 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.49 % Allowed : 24.72 % Favored : 70.79 % 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: 3.07 (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 0.012 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 227 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 207 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9175 (mp) REVERT: B 82 GLN cc_start: 0.9514 (mm110) cc_final: 0.9144 (mm-40) REVERT: B 95 GLN cc_start: 0.9181 (mp10) cc_final: 0.8850 (mp10) REVERT: B 101 ASP cc_start: 0.9644 (t0) cc_final: 0.9158 (m-30) REVERT: B 104 LYS cc_start: 0.9440 (ttmm) cc_final: 0.9106 (mtmm) REVERT: B 195 MET cc_start: 0.4445 (ttp) cc_final: 0.3949 (tpp) REVERT: B 231 GLN cc_start: 0.8989 (tt0) cc_final: 0.8271 (tt0) REVERT: B 240 GLU cc_start: 0.8480 (mt-10) cc_final: 0.7924 (pt0) REVERT: B 270 TYR cc_start: 0.8385 (t80) cc_final: 0.8011 (t80) REVERT: B 289 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8512 (mp) REVERT: A 42 MET cc_start: 0.8433 (mmm) cc_final: 0.8180 (mmm) REVERT: A 48 LEU cc_start: 0.9495 (tp) cc_final: 0.9248 (tp) REVERT: A 51 PHE cc_start: 0.9178 (t80) cc_final: 0.8958 (t80) REVERT: A 52 LEU cc_start: 0.9554 (mt) cc_final: 0.9347 (mt) REVERT: A 56 LEU cc_start: 0.9623 (tp) cc_final: 0.9422 (tp) REVERT: A 104 LYS cc_start: 0.9555 (ttpp) cc_final: 0.9287 (mtmm) REVERT: A 122 GLN cc_start: 0.8801 (pm20) cc_final: 0.8476 (pm20) REVERT: A 263 GLU cc_start: 0.8534 (pp20) cc_final: 0.8306 (pp20) REVERT: A 268 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7522 (p0) REVERT: A 269 TYR cc_start: 0.8468 (m-80) cc_final: 0.7902 (m-80) outliers start: 20 outliers final: 12 residues processed: 211 average time/residue: 0.2084 time to fit residues: 56.0954 Evaluate side-chains 214 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 199 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 282 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 20 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 41 optimal weight: 6.9990 chunk 10 optimal weight: 0.0980 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3979 r_free = 0.3979 target = 0.151332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.100876 restraints weight = 7410.346| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 4.33 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4272 Z= 0.236 Angle : 0.727 8.160 5803 Z= 0.360 Chirality : 0.043 0.247 688 Planarity : 0.005 0.063 692 Dihedral : 5.858 42.030 611 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.49 % Allowed : 28.09 % Favored : 67.42 % 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: 2.84 (0.36), residues: 522 helix: 2.62 (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 0.010 0.001 TRP B 44 HIS 0.003 0.001 HIS A 91 PHE 0.017 0.001 PHE B 158 TYR 0.013 0.002 TYR A 284 ARG 0.005 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 233 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 213 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 GLN cc_start: 0.9523 (mm110) cc_final: 0.9217 (mm-40) REVERT: B 95 GLN cc_start: 0.9150 (mp10) cc_final: 0.8871 (mp10) REVERT: B 101 ASP cc_start: 0.9641 (t0) cc_final: 0.9240 (m-30) REVERT: B 104 LYS cc_start: 0.9467 (ttmm) cc_final: 0.9172 (mtmm) REVERT: B 195 MET cc_start: 0.4177 (ttp) cc_final: 0.3801 (tpp) REVERT: B 231 GLN cc_start: 0.8950 (tt0) cc_final: 0.8215 (tt0) REVERT: B 270 TYR cc_start: 0.8332 (t80) cc_final: 0.8034 (t80) REVERT: B 289 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8644 (mp) REVERT: A 42 MET cc_start: 0.8525 (mmm) cc_final: 0.8298 (mmm) REVERT: A 48 LEU cc_start: 0.9480 (tp) cc_final: 0.9231 (tp) REVERT: A 51 PHE cc_start: 0.9173 (t80) cc_final: 0.8965 (t80) REVERT: A 52 LEU cc_start: 0.9554 (mt) cc_final: 0.9330 (mt) REVERT: A 56 LEU cc_start: 0.9618 (tp) cc_final: 0.9414 (tp) REVERT: A 104 LYS cc_start: 0.9548 (ttpp) cc_final: 0.9246 (mtmm) REVERT: A 115 ASN cc_start: 0.8624 (t0) cc_final: 0.8382 (t0) REVERT: A 122 GLN cc_start: 0.8838 (pm20) cc_final: 0.8432 (pm20) REVERT: A 151 HIS cc_start: 0.8573 (m90) cc_final: 0.7932 (m90) REVERT: A 240 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8202 (mt-10) REVERT: A 263 GLU cc_start: 0.8605 (pp20) cc_final: 0.8371 (pp20) REVERT: A 268 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7556 (p0) REVERT: A 269 TYR cc_start: 0.8419 (m-80) cc_final: 0.7791 (m-80) outliers start: 20 outliers final: 13 residues processed: 217 average time/residue: 0.1687 time to fit residues: 46.3815 Evaluate side-chains 221 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 206 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 289 LEU Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.149825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.100484 restraints weight = 7280.388| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 4.16 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 4272 Z= 0.265 Angle : 0.773 13.069 5803 Z= 0.378 Chirality : 0.043 0.195 688 Planarity : 0.005 0.065 692 Dihedral : 5.842 46.295 611 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.49 % Allowed : 31.69 % Favored : 63.82 % 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: 2.65 (0.36), residues: 522 helix: 2.46 (0.24), residues: 410 sheet: None (None), residues: 0 loop : -1.06 (0.60), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 277 HIS 0.004 0.001 HIS A 91 PHE 0.020 0.002 PHE B 51 TYR 0.012 0.002 TYR A 270 ARG 0.006 0.001 ARG A 297 *********************** 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 : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 GLN cc_start: 0.9508 (mm110) cc_final: 0.9107 (tp40) REVERT: B 101 ASP cc_start: 0.9657 (t0) cc_final: 0.9298 (m-30) REVERT: B 104 LYS cc_start: 0.9455 (ttmm) cc_final: 0.9196 (mtmm) REVERT: B 195 MET cc_start: 0.4155 (ttp) cc_final: 0.3907 (tpp) REVERT: B 231 GLN cc_start: 0.8922 (tt0) cc_final: 0.8171 (tt0) REVERT: B 240 GLU cc_start: 0.8459 (mt-10) cc_final: 0.7924 (pt0) REVERT: B 270 TYR cc_start: 0.8345 (t80) cc_final: 0.8052 (t80) REVERT: B 289 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8609 (mp) REVERT: A 48 LEU cc_start: 0.9469 (tp) cc_final: 0.9217 (tp) REVERT: A 51 PHE cc_start: 0.9129 (t80) cc_final: 0.8929 (t80) REVERT: A 52 LEU cc_start: 0.9554 (mt) cc_final: 0.9328 (mt) REVERT: A 79 ARG cc_start: 0.9358 (OUTLIER) cc_final: 0.9113 (ptm160) REVERT: A 98 GLU cc_start: 0.9525 (OUTLIER) cc_final: 0.9107 (pm20) REVERT: A 104 LYS cc_start: 0.9511 (ttpp) cc_final: 0.9248 (mtmm) REVERT: A 115 ASN cc_start: 0.8633 (t0) cc_final: 0.8359 (t0) REVERT: A 122 GLN cc_start: 0.8844 (pm20) cc_final: 0.8463 (pm20) REVERT: A 151 HIS cc_start: 0.8580 (m90) cc_final: 0.7856 (m90) REVERT: A 240 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8226 (mt-10) REVERT: A 263 GLU cc_start: 0.8702 (pp20) cc_final: 0.8445 (pp20) REVERT: A 268 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7547 (p0) REVERT: A 269 TYR cc_start: 0.8491 (m-80) cc_final: 0.7793 (m-80) outliers start: 20 outliers final: 14 residues processed: 209 average time/residue: 0.1452 time to fit residues: 38.7637 Evaluate side-chains 218 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 200 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 98 GLU 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 268 ASP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.7980 chunk 8 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.151148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.105426 restraints weight = 7252.265| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 4.01 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 4272 Z= 0.268 Angle : 0.850 13.914 5803 Z= 0.409 Chirality : 0.044 0.180 688 Planarity : 0.005 0.064 692 Dihedral : 5.827 48.278 611 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.94 % Allowed : 33.26 % Favored : 61.80 % 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: 2.37 (0.24), residues: 410 sheet: None (None), residues: 0 loop : -1.11 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 277 HIS 0.004 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 *********************** 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 225 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 203 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ARG cc_start: 0.9138 (mtp-110) cc_final: 0.8821 (ttp-110) REVERT: B 82 GLN cc_start: 0.9482 (mm110) cc_final: 0.9080 (tp40) REVERT: B 101 ASP cc_start: 0.9642 (t0) cc_final: 0.9264 (m-30) REVERT: B 104 LYS cc_start: 0.9464 (ttmm) cc_final: 0.9208 (mtmm) REVERT: B 195 MET cc_start: 0.4130 (ttp) cc_final: 0.3866 (tpp) REVERT: B 231 GLN cc_start: 0.8932 (tt0) cc_final: 0.8182 (tt0) REVERT: B 240 GLU cc_start: 0.8460 (mt-10) cc_final: 0.7928 (pt0) REVERT: B 270 TYR cc_start: 0.8375 (t80) cc_final: 0.8116 (t80) REVERT: B 289 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8607 (mp) REVERT: A 42 MET cc_start: 0.8394 (mmm) cc_final: 0.8067 (mmp) REVERT: A 48 LEU cc_start: 0.9489 (tp) cc_final: 0.9239 (tp) REVERT: A 52 LEU cc_start: 0.9567 (mt) cc_final: 0.9341 (mt) REVERT: A 79 ARG cc_start: 0.9343 (OUTLIER) cc_final: 0.9100 (ptm160) REVERT: A 100 GLU cc_start: 0.9415 (mm-30) cc_final: 0.8977 (mm-30) REVERT: A 104 LYS cc_start: 0.9513 (ttpp) cc_final: 0.9235 (mtmm) REVERT: A 115 ASN cc_start: 0.8737 (t0) cc_final: 0.8443 (t0) REVERT: A 122 GLN cc_start: 0.8893 (pm20) cc_final: 0.8544 (pm20) REVERT: A 151 HIS cc_start: 0.8606 (m90) cc_final: 0.8090 (m170) REVERT: A 172 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.8387 (t80) REVERT: A 240 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8231 (mt-10) REVERT: A 263 GLU cc_start: 0.8725 (pp20) cc_final: 0.8468 (pp20) REVERT: A 268 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7510 (p0) REVERT: A 269 TYR cc_start: 0.8490 (m-80) cc_final: 0.7760 (m-80) outliers start: 22 outliers final: 15 residues processed: 206 average time/residue: 0.1427 time to fit residues: 37.4957 Evaluate side-chains 219 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 200 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 282 LEU 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 6 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 45 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3929 r_free = 0.3929 target = 0.148573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.097588 restraints weight = 7256.622| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 4.13 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4272 Z= 0.267 Angle : 0.875 13.929 5803 Z= 0.422 Chirality : 0.046 0.228 688 Planarity : 0.005 0.065 692 Dihedral : 5.767 50.542 611 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.94 % Allowed : 32.58 % Favored : 62.47 % 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: 2.37 (0.36), residues: 522 helix: 2.26 (0.24), residues: 410 sheet: None (None), residues: 0 loop : -1.10 (0.58), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 277 HIS 0.003 0.001 HIS A 151 PHE 0.020 0.001 PHE B 51 TYR 0.012 0.002 TYR A 270 ARG 0.006 0.001 ARG A 297 *********************** 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 227 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ARG cc_start: 0.9195 (mtp-110) cc_final: 0.8891 (ttp-110) REVERT: B 82 GLN cc_start: 0.9510 (mm110) cc_final: 0.9085 (tp40) REVERT: B 101 ASP cc_start: 0.9653 (t0) cc_final: 0.9277 (m-30) REVERT: B 104 LYS cc_start: 0.9464 (ttmm) cc_final: 0.9225 (mtmm) REVERT: B 195 MET cc_start: 0.4271 (ttp) cc_final: 0.3890 (tpp) REVERT: B 231 GLN cc_start: 0.8917 (tt0) cc_final: 0.8190 (tt0) REVERT: B 240 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8078 (pt0) REVERT: B 289 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8619 (mp) REVERT: A 48 LEU cc_start: 0.9472 (tp) cc_final: 0.9266 (tp) REVERT: A 52 LEU cc_start: 0.9565 (mt) cc_final: 0.9295 (mt) REVERT: A 79 ARG cc_start: 0.9364 (OUTLIER) cc_final: 0.9121 (ptm-80) REVERT: A 95 GLN cc_start: 0.8881 (mp10) cc_final: 0.8615 (mp10) REVERT: A 100 GLU cc_start: 0.9458 (mm-30) cc_final: 0.9119 (mm-30) REVERT: A 115 ASN cc_start: 0.8694 (t0) cc_final: 0.8394 (t0) REVERT: A 122 GLN cc_start: 0.8923 (pm20) cc_final: 0.8542 (pm20) REVERT: A 151 HIS cc_start: 0.8613 (m90) cc_final: 0.8105 (m170) REVERT: A 172 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8406 (t80) REVERT: A 240 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8211 (mt-10) REVERT: A 263 GLU cc_start: 0.8756 (pp20) cc_final: 0.8485 (pp20) REVERT: A 268 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7539 (p0) REVERT: A 269 TYR cc_start: 0.8521 (m-80) cc_final: 0.7831 (m-80) outliers start: 22 outliers final: 15 residues processed: 208 average time/residue: 0.1381 time to fit residues: 36.5512 Evaluate side-chains 221 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 202 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 289 LEU Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 7 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 42 optimal weight: 20.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.149112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.102277 restraints weight = 7255.215| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.94 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.5071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 4272 Z= 0.286 Angle : 0.907 14.268 5803 Z= 0.437 Chirality : 0.045 0.243 688 Planarity : 0.005 0.065 692 Dihedral : 5.824 50.764 611 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.27 % Allowed : 35.73 % 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: 2.33 (0.36), residues: 522 helix: 2.20 (0.24), residues: 409 sheet: None (None), residues: 0 loop : -0.95 (0.58), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 127 HIS 0.004 0.001 HIS A 91 PHE 0.046 0.002 PHE A 196 TYR 0.023 0.002 TYR B 270 ARG 0.005 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 221 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 202 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: B 79 ARG cc_start: 0.9197 (mtp-110) cc_final: 0.8874 (ttp-110) REVERT: B 82 GLN cc_start: 0.9496 (mm110) cc_final: 0.9075 (tp40) REVERT: B 101 ASP cc_start: 0.9621 (t0) cc_final: 0.9274 (m-30) REVERT: B 104 LYS cc_start: 0.9508 (ttmm) cc_final: 0.9255 (mtmm) REVERT: B 195 MET cc_start: 0.4389 (ttp) cc_final: 0.3828 (tpp) REVERT: B 240 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8090 (pt0) REVERT: B 289 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8637 (mp) REVERT: A 42 MET cc_start: 0.8516 (mmm) cc_final: 0.8207 (mmp) REVERT: A 48 LEU cc_start: 0.9495 (tp) cc_final: 0.9284 (tp) REVERT: A 52 LEU cc_start: 0.9566 (mt) cc_final: 0.9295 (mt) REVERT: A 79 ARG cc_start: 0.9360 (OUTLIER) cc_final: 0.9127 (ptm-80) REVERT: A 100 GLU cc_start: 0.9409 (mm-30) cc_final: 0.9064 (mm-30) REVERT: A 115 ASN cc_start: 0.8802 (t0) cc_final: 0.8517 (t0) REVERT: A 122 GLN cc_start: 0.8941 (pm20) cc_final: 0.8564 (pm20) REVERT: A 151 HIS cc_start: 0.8651 (m90) cc_final: 0.8160 (m170) REVERT: A 207 ARG cc_start: 0.8724 (tmt170) cc_final: 0.8451 (tpt90) REVERT: A 240 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8218 (mt-10) REVERT: A 263 GLU cc_start: 0.8724 (pp20) cc_final: 0.8427 (pp20) REVERT: A 268 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7429 (p0) REVERT: A 269 TYR cc_start: 0.8478 (m-80) cc_final: 0.7725 (m-80) outliers start: 19 outliers final: 15 residues processed: 204 average time/residue: 0.1372 time to fit residues: 35.8027 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 : 0.467 ------------------------------------------------------------------------------- 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 289 LEU 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 219 CYS Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 20 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 49 optimal weight: 0.0570 chunk 23 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.150636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.101674 restraints weight = 7316.685| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 4.18 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.5229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 4272 Z= 0.279 Angle : 0.943 14.446 5803 Z= 0.451 Chirality : 0.047 0.251 688 Planarity : 0.005 0.065 692 Dihedral : 5.804 53.864 611 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.49 % Allowed : 35.96 % 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: 2.23 (0.36), residues: 522 helix: 2.13 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.94 (0.59), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 277 HIS 0.003 0.001 HIS A 151 PHE 0.027 0.001 PHE A 51 TYR 0.014 0.002 TYR A 270 ARG 0.006 0.001 ARG A 297 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 ARG cc_start: 0.9210 (mtp-110) cc_final: 0.8921 (ttp-110) REVERT: B 82 GLN cc_start: 0.9502 (mm110) cc_final: 0.9089 (tp40) REVERT: B 101 ASP cc_start: 0.9619 (t0) cc_final: 0.9277 (m-30) REVERT: B 104 LYS cc_start: 0.9523 (ttmm) cc_final: 0.9262 (mtmm) REVERT: B 195 MET cc_start: 0.4357 (ttp) cc_final: 0.3958 (tpp) REVERT: B 231 GLN cc_start: 0.8865 (tt0) cc_final: 0.8149 (tt0) REVERT: B 240 GLU cc_start: 0.8482 (mt-10) cc_final: 0.7974 (pt0) REVERT: A 42 MET cc_start: 0.8532 (mmm) cc_final: 0.8206 (mmp) REVERT: A 48 LEU cc_start: 0.9482 (tp) cc_final: 0.9270 (tp) REVERT: A 52 LEU cc_start: 0.9551 (mt) cc_final: 0.9286 (mt) REVERT: A 79 ARG cc_start: 0.9375 (OUTLIER) cc_final: 0.9146 (ptm-80) REVERT: A 100 GLU cc_start: 0.9424 (mm-30) cc_final: 0.9016 (mm-30) REVERT: A 115 ASN cc_start: 0.8758 (t0) cc_final: 0.8480 (t0) REVERT: A 122 GLN cc_start: 0.9002 (pm20) cc_final: 0.8623 (pm20) REVERT: A 151 HIS cc_start: 0.8631 (m90) cc_final: 0.8144 (m170) REVERT: A 172 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8373 (t80) REVERT: A 207 ARG cc_start: 0.8733 (tmt170) cc_final: 0.8455 (tpt90) REVERT: A 240 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8178 (mt-10) REVERT: A 263 GLU cc_start: 0.8859 (pp20) cc_final: 0.8565 (pp20) REVERT: A 268 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.7443 (p0) REVERT: A 269 TYR cc_start: 0.8557 (m-80) cc_final: 0.7817 (m-80) outliers start: 20 outliers final: 16 residues processed: 201 average time/residue: 0.1381 time to fit residues: 35.4199 Evaluate side-chains 214 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 195 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 A residue 79 ARG Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 95 GLN 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 278 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 46 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 28 optimal weight: 0.0980 chunk 39 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.150463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.100575 restraints weight = 7424.788| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 4.19 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.5270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4272 Z= 0.267 Angle : 0.960 13.248 5803 Z= 0.459 Chirality : 0.048 0.259 688 Planarity : 0.005 0.061 692 Dihedral : 5.821 55.249 611 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.60 % Allowed : 36.85 % 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: 2.11 (0.36), residues: 522 helix: 2.06 (0.24), residues: 405 sheet: None (None), residues: 0 loop : -1.02 (0.57), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 277 HIS 0.003 0.001 HIS A 151 PHE 0.058 0.002 PHE A 196 TYR 0.026 0.002 TYR B 270 ARG 0.004 0.001 ARG B 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2230.42 seconds wall clock time: 40 minutes 11.42 seconds (2411.42 seconds total)