Starting phenix.real_space_refine on Thu Sep 18 04:51:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tt6_26112/09_2025/7tt6_26112.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tt6_26112/09_2025/7tt6_26112.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tt6_26112/09_2025/7tt6_26112.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tt6_26112/09_2025/7tt6_26112.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tt6_26112/09_2025/7tt6_26112.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tt6_26112/09_2025/7tt6_26112.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.005 sd= 0.054 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 S 27 5.16 5 C 4562 2.51 5 N 1221 2.21 5 O 1398 1.98 5 H 6839 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14047 Number of models: 1 Model: "" Number of chains: 5 Chain: "P" Number of atoms: 2271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 2271 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 147} Chain breaks: 7 Chain: "A" Number of atoms: 7687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 7687 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 21, 'TRANS': 480} Chain breaks: 3 Chain: "C" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 484 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 4, 'TRANS': 29} Chain: "D" Number of atoms: 2223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2223 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain breaks: 3 Chain: "E" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1382 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Time building chain proxies: 2.82, per 1000 atoms: 0.20 Number of scatterers: 14047 At special positions: 0 Unit cell: (93.4223, 95.57, 135.301, 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) S 27 16.00 O 1398 8.00 N 1221 7.00 C 4562 6.00 H 6839 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS P1299 " - pdb=" SG CYS A 425 " distance=2.04 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " 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: 1.15 Conformation dependent library (CDL) restraints added in 425.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1658 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 7 sheets defined 23.7% alpha, 42.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 280 through 289 removed outlier: 4.129A pdb=" N ILE A 284 " --> pdb=" O HIS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 313 Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.877A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 391 removed outlier: 4.324A pdb=" N GLY A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LYS A 386 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.650A pdb=" N GLY A 451 " --> pdb=" O ASN A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 726 through 731 Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'D' and resid 47 through 57 Processing helix chain 'D' and resid 77 through 82 Processing helix chain 'D' and resid 84 through 91 Processing helix chain 'D' and resid 114 through 120 Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 135 removed outlier: 4.476A pdb=" N ASP D 134 " --> pdb=" O ASP D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 165 through 189 removed outlier: 3.529A pdb=" N PHE D 169 " --> pdb=" O LYS D 165 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR D 177 " --> pdb=" O ARG D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 222 removed outlier: 3.802A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 241 Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 51 through 60 Processing sheet with id=AA1, first strand: chain 'P' and resid 1039 through 1046 removed outlier: 4.078A pdb=" N HIS P1062 " --> pdb=" O MET P1046 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA P1165 " --> pdb=" O VAL P1161 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 1039 through 1046 removed outlier: 4.078A pdb=" N HIS P1062 " --> pdb=" O MET P1046 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA P1291 " --> pdb=" O GLU P1279 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA P1294 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 430 " --> pdb=" O ALA P1294 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 273 through 276 Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 355 removed outlier: 7.968A pdb=" N VAL A 414 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ILE A 352 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N TYR A 416 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N PHE A 354 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N VAL A 418 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS A 419 " --> pdb=" O THR A 397 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 671 through 674 removed outlier: 4.620A pdb=" N ALA A 672 " --> pdb=" O SER A 702 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.700A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 32 through 35 removed outlier: 6.689A pdb=" N THR E 90 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASN E 106 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N THR E 92 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE E 104 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR E 94 " --> pdb=" O THR E 102 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1206 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: 3.74 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 6839 1.04 - 1.24: 909 1.24 - 1.44: 2453 1.44 - 1.64: 3960 1.64 - 1.84: 50 Bond restraints: 14211 Sorted by residual: bond pdb=" CB TRP A 739 " pdb=" CG TRP A 739 " ideal model delta sigma weight residual 1.498 1.458 0.040 3.10e-02 1.04e+03 1.69e+00 bond pdb=" CG ARG A 366 " pdb=" CD ARG A 366 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.68e+00 bond pdb=" CB TRP A 376 " pdb=" CG TRP A 376 " ideal model delta sigma weight residual 1.498 1.458 0.040 3.10e-02 1.04e+03 1.65e+00 bond pdb=" CA THR D 186 " pdb=" C THR D 186 " ideal model delta sigma weight residual 1.523 1.507 0.016 1.30e-02 5.92e+03 1.53e+00 bond pdb=" C THR A 720 " pdb=" O THR A 720 " ideal model delta sigma weight residual 1.235 1.251 -0.015 1.29e-02 6.01e+03 1.44e+00 ... (remaining 14206 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 24756 1.86 - 3.73: 609 3.73 - 5.59: 51 5.59 - 7.46: 8 7.46 - 9.32: 2 Bond angle restraints: 25426 Sorted by residual: angle pdb=" N PHE A 478 " pdb=" CA PHE A 478 " pdb=" C PHE A 478 " ideal model delta sigma weight residual 113.12 107.69 5.43 1.25e+00 6.40e-01 1.89e+01 angle pdb=" N MET D 225 " pdb=" CA MET D 225 " pdb=" C MET D 225 " ideal model delta sigma weight residual 109.96 102.81 7.15 1.68e+00 3.54e-01 1.81e+01 angle pdb=" CA CYS A 690 " pdb=" CB CYS A 690 " pdb=" SG CYS A 690 " ideal model delta sigma weight residual 114.40 123.72 -9.32 2.30e+00 1.89e-01 1.64e+01 angle pdb=" C ARG A 734 " pdb=" N THR A 735 " pdb=" CA THR A 735 " ideal model delta sigma weight residual 122.59 116.46 6.13 1.57e+00 4.06e-01 1.53e+01 angle pdb=" CA CYS A 700 " pdb=" CB CYS A 700 " pdb=" SG CYS A 700 " ideal model delta sigma weight residual 114.40 122.69 -8.29 2.30e+00 1.89e-01 1.30e+01 ... (remaining 25421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 6416 18.00 - 35.99: 217 35.99 - 53.99: 103 53.99 - 71.98: 38 71.98 - 89.98: 7 Dihedral angle restraints: 6781 sinusoidal: 3577 harmonic: 3204 Sorted by residual: dihedral pdb=" CA LEU A 377 " pdb=" C LEU A 377 " pdb=" N GLY A 378 " pdb=" CA GLY A 378 " ideal model delta harmonic sigma weight residual 180.00 161.30 18.70 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA TYR A 688 " pdb=" C TYR A 688 " pdb=" N GLU A 689 " pdb=" CA GLU A 689 " ideal model delta harmonic sigma weight residual -180.00 -161.47 -18.53 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ASP P1270 " pdb=" C ASP P1270 " pdb=" N ASN P1271 " pdb=" CA ASN P1271 " ideal model delta harmonic sigma weight residual -180.00 -163.01 -16.99 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 6778 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 685 0.037 - 0.074: 227 0.074 - 0.110: 96 0.110 - 0.147: 31 0.147 - 0.184: 7 Chirality restraints: 1046 Sorted by residual: chirality pdb=" CA VAL A 744 " pdb=" N VAL A 744 " pdb=" C VAL A 744 " pdb=" CB VAL A 744 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.44e-01 chirality pdb=" CA ILE P1167 " pdb=" N ILE P1167 " pdb=" C ILE P1167 " pdb=" CB ILE P1167 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.16e-01 chirality pdb=" CA ARG D 223 " pdb=" N ARG D 223 " pdb=" C ARG D 223 " pdb=" CB ARG D 223 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.06e-01 ... (remaining 1043 not shown) Planarity restraints: 2171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 167 " -0.022 2.00e-02 2.50e+03 4.34e-02 1.89e+01 pdb=" C LEU D 167 " 0.075 2.00e-02 2.50e+03 pdb=" O LEU D 167 " -0.028 2.00e-02 2.50e+03 pdb=" N VAL D 168 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 166 " 0.021 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C ARG D 166 " -0.071 2.00e-02 2.50e+03 pdb=" O ARG D 166 " 0.026 2.00e-02 2.50e+03 pdb=" N LEU D 167 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU P1168 " 0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C GLU P1168 " -0.070 2.00e-02 2.50e+03 pdb=" O GLU P1168 " 0.026 2.00e-02 2.50e+03 pdb=" N PRO P1169 " 0.024 2.00e-02 2.50e+03 ... (remaining 2168 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 258 2.08 - 2.71: 23218 2.71 - 3.34: 37093 3.34 - 3.97: 48065 3.97 - 4.60: 74500 Nonbonded interactions: 183134 Sorted by model distance: nonbonded pdb=" HD1 HIS A 533 " pdb=" OD1 ASP A 568 " model vdw 1.453 2.450 nonbonded pdb=" OE1 GLN D 209 " pdb="HH21 ARG D 212 " model vdw 1.551 2.450 nonbonded pdb=" OD2 ASP A 582 " pdb=" HG1 THR A 588 " model vdw 1.558 2.450 nonbonded pdb=" OD1 ASP A 569 " pdb=" H ASN A 606 " model vdw 1.566 2.450 nonbonded pdb=" OD1 ASP D 136 " pdb=" H GLN D 138 " model vdw 1.576 2.450 ... (remaining 183129 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.290 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: 0.090 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.370 Find NCS groups from input model: 0.050 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 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 : 0.005 0.040 7374 Z= 0.245 Angle : 0.913 9.320 9987 Z= 0.557 Chirality : 0.047 0.184 1046 Planarity : 0.006 0.070 1309 Dihedral : 10.729 89.977 2628 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.26), residues: 879 helix: -1.55 (0.31), residues: 178 sheet: 1.23 (0.25), residues: 345 loop : 0.42 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 135 TYR 0.023 0.002 TYR A 585 PHE 0.016 0.002 PHE A 791 TRP 0.018 0.002 TRP A 449 HIS 0.008 0.003 HIS A 555 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 7372) covalent geometry : angle 0.90963 ( 9983) SS BOND : bond 0.00395 ( 2) SS BOND : angle 3.87000 ( 4) hydrogen bonds : bond 0.12900 ( 394) hydrogen bonds : angle 7.73821 ( 1206) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 0.403 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: 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: 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: 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: P 1260 MET cc_start: 0.4627 (mtm) cc_final: 0.4350 (mpp) REVERT: A 307 ASP cc_start: 0.8373 (m-30) cc_final: 0.8075 (m-30) REVERT: A 422 ASN cc_start: 0.7854 (m-40) cc_final: 0.7569 (m-40) REVERT: A 542 GLN cc_start: 0.8887 (mt0) cc_final: 0.8671 (mm-40) REVERT: A 557 SER cc_start: 0.8992 (m) cc_final: 0.8623 (t) REVERT: A 633 THR cc_start: 0.8382 (p) cc_final: 0.8061 (p) REVERT: A 768 MET cc_start: 0.7980 (mtt) cc_final: 0.7521 (mtm) REVERT: A 805 ASN cc_start: 0.8545 (t0) cc_final: 0.7858 (p0) REVERT: D 127 PHE cc_start: 0.8668 (t80) cc_final: 0.8459 (t80) REVERT: D 208 THR cc_start: 0.9142 (t) cc_final: 0.8925 (t) REVERT: D 228 ASN cc_start: 0.8670 (m-40) cc_final: 0.8306 (m-40) REVERT: E 31 ASP cc_start: 0.8285 (m-30) cc_final: 0.7644 (p0) REVERT: E 41 ASN cc_start: 0.9062 (m-40) cc_final: 0.8725 (t0) REVERT: E 43 VAL cc_start: 0.9383 (t) cc_final: 0.9144 (t) REVERT: E 64 MET cc_start: 0.8471 (mtp) cc_final: 0.8233 (mtm) REVERT: E 80 GLN cc_start: 0.8626 (tp40) cc_final: 0.8311 (tp40) REVERT: E 81 PRO cc_start: 0.8877 (Cg_exo) cc_final: 0.8401 (Cg_endo) REVERT: E 86 VAL cc_start: 0.8833 (p) cc_final: 0.8624 (p) REVERT: E 95 PHE cc_start: 0.8396 (m-80) cc_final: 0.8141 (m-80) REVERT: E 103 ASN cc_start: 0.9095 (t0) cc_final: 0.8778 (t0) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.2136 time to fit residues: 81.7977 Evaluate side-chains 198 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 40.0000 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN D 230 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.155300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.099660 restraints weight = 40879.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.104867 restraints weight = 18566.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.108179 restraints weight = 12011.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.110190 restraints weight = 9427.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.110942 restraints weight = 8221.596| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 7374 Z= 0.162 Angle : 0.594 7.589 9987 Z= 0.336 Chirality : 0.044 0.182 1046 Planarity : 0.004 0.040 1309 Dihedral : 4.664 37.593 1003 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.27 % Allowed : 1.47 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.27), residues: 879 helix: 0.32 (0.36), residues: 187 sheet: 0.68 (0.24), residues: 370 loop : 0.52 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 321 TYR 0.020 0.001 TYR D 184 PHE 0.014 0.001 PHE A 738 TRP 0.009 0.001 TRP A 576 HIS 0.003 0.001 HIS C 51 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 7372) covalent geometry : angle 0.58648 ( 9983) SS BOND : bond 0.00854 ( 2) SS BOND : angle 4.76568 ( 4) hydrogen bonds : bond 0.04736 ( 394) hydrogen bonds : angle 6.13582 ( 1206) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 229 time to evaluate : 0.304 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: 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: 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: 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: symmetry clash REVERT: P 1119 ILE cc_start: 0.8786 (mt) cc_final: 0.8551 (tp) REVERT: P 1271 ASN cc_start: 0.8479 (p0) cc_final: 0.7806 (p0) REVERT: P 1292 VAL cc_start: 0.8140 (p) cc_final: 0.7853 (m) REVERT: A 283 GLU cc_start: 0.9280 (mp0) cc_final: 0.8671 (mt-10) REVERT: A 288 THR cc_start: 0.9197 (m) cc_final: 0.8906 (p) REVERT: A 422 ASN cc_start: 0.8263 (m-40) cc_final: 0.8008 (m-40) REVERT: A 426 PHE cc_start: 0.8797 (t80) cc_final: 0.8498 (t80) REVERT: A 445 GLN cc_start: 0.8324 (pp30) cc_final: 0.7753 (pm20) REVERT: A 446 GLN cc_start: 0.8663 (mt0) cc_final: 0.8412 (mt0) REVERT: A 447 ASP cc_start: 0.8051 (t0) cc_final: 0.7837 (t0) REVERT: A 542 GLN cc_start: 0.8992 (mt0) cc_final: 0.8681 (mm-40) REVERT: A 557 SER cc_start: 0.8981 (m) cc_final: 0.8614 (t) REVERT: A 648 PHE cc_start: 0.9100 (p90) cc_final: 0.8896 (p90) REVERT: A 768 MET cc_start: 0.8205 (mtt) cc_final: 0.7869 (mtm) REVERT: D 84 ASP cc_start: 0.8084 (m-30) cc_final: 0.7568 (m-30) REVERT: D 207 ASP cc_start: 0.7895 (m-30) cc_final: 0.7121 (m-30) REVERT: E 31 ASP cc_start: 0.8338 (m-30) cc_final: 0.8084 (m-30) REVERT: E 38 LEU cc_start: 0.8493 (tt) cc_final: 0.8249 (tt) outliers start: 2 outliers final: 0 residues processed: 229 average time/residue: 0.2084 time to fit residues: 61.6753 Evaluate side-chains 194 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 36 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 4 optimal weight: 40.0000 chunk 9 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 8 optimal weight: 30.0000 chunk 26 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.4006 r_free = 0.4006 target = 0.154734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.099036 restraints weight = 40585.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.104422 restraints weight = 17872.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.107774 restraints weight = 11327.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.109806 restraints weight = 8807.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.110669 restraints weight = 7672.879| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7374 Z= 0.141 Angle : 0.532 4.878 9987 Z= 0.300 Chirality : 0.043 0.174 1046 Planarity : 0.005 0.058 1309 Dihedral : 4.362 24.946 1003 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.27), residues: 879 helix: 0.76 (0.36), residues: 187 sheet: 0.40 (0.24), residues: 374 loop : 0.54 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 421 TYR 0.015 0.001 TYR D 184 PHE 0.013 0.001 PHE D 144 TRP 0.010 0.001 TRP A 576 HIS 0.001 0.000 HIS C 51 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 7372) covalent geometry : angle 0.52890 ( 9983) SS BOND : bond 0.00571 ( 2) SS BOND : angle 3.05930 ( 4) hydrogen bonds : bond 0.04083 ( 394) hydrogen bonds : angle 5.68365 ( 1206) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.330 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1271 ASN cc_start: 0.8354 (p0) cc_final: 0.7795 (p0) REVERT: A 369 MET cc_start: 0.8753 (mmt) cc_final: 0.8111 (mmt) REVERT: A 422 ASN cc_start: 0.8249 (m-40) cc_final: 0.7945 (m-40) REVERT: A 445 GLN cc_start: 0.8371 (pp30) cc_final: 0.7789 (pm20) REVERT: A 446 GLN cc_start: 0.8663 (mt0) cc_final: 0.8430 (mt0) REVERT: A 447 ASP cc_start: 0.8035 (t0) cc_final: 0.7781 (t0) REVERT: A 533 HIS cc_start: 0.8844 (t70) cc_final: 0.8604 (t70) REVERT: A 542 GLN cc_start: 0.9055 (mt0) cc_final: 0.8792 (mm-40) REVERT: A 557 SER cc_start: 0.8954 (m) cc_final: 0.8551 (t) REVERT: A 648 PHE cc_start: 0.9109 (p90) cc_final: 0.8881 (p90) REVERT: A 727 ASP cc_start: 0.8886 (p0) cc_final: 0.8579 (p0) REVERT: A 768 MET cc_start: 0.8237 (mtt) cc_final: 0.7931 (mtm) REVERT: D 84 ASP cc_start: 0.8085 (m-30) cc_final: 0.7519 (m-30) REVERT: D 127 PHE cc_start: 0.8586 (t80) cc_final: 0.8384 (t80) REVERT: D 136 ASP cc_start: 0.9305 (t0) cc_final: 0.9105 (t70) REVERT: D 207 ASP cc_start: 0.7608 (m-30) cc_final: 0.7133 (m-30) REVERT: D 228 ASN cc_start: 0.8354 (m110) cc_final: 0.8029 (m110) REVERT: E 31 ASP cc_start: 0.8366 (m-30) cc_final: 0.8044 (m-30) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1884 time to fit residues: 54.3580 Evaluate side-chains 192 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 7 optimal weight: 50.0000 chunk 47 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 65 optimal weight: 0.0570 chunk 63 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.153355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.097840 restraints weight = 41048.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.103028 restraints weight = 18213.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.106314 restraints weight = 11648.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.108206 restraints weight = 9088.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.109200 restraints weight = 7970.313| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.5008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7374 Z= 0.162 Angle : 0.544 8.410 9987 Z= 0.303 Chirality : 0.042 0.172 1046 Planarity : 0.004 0.048 1309 Dihedral : 4.293 20.336 1003 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.27), residues: 879 helix: 0.79 (0.37), residues: 188 sheet: 0.11 (0.24), residues: 374 loop : 0.32 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P1269 TYR 0.022 0.001 TYR A 585 PHE 0.015 0.001 PHE E 95 TRP 0.010 0.001 TRP A 576 HIS 0.001 0.000 HIS C 51 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 7372) covalent geometry : angle 0.53923 ( 9983) SS BOND : bond 0.01013 ( 2) SS BOND : angle 3.59606 ( 4) hydrogen bonds : bond 0.03782 ( 394) hydrogen bonds : angle 5.53720 ( 1206) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.301 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1260 MET cc_start: 0.5250 (mpp) cc_final: 0.5030 (mpp) REVERT: P 1270 ASP cc_start: 0.8628 (t70) cc_final: 0.8292 (t0) REVERT: P 1271 ASN cc_start: 0.8454 (p0) cc_final: 0.8043 (p0) REVERT: A 369 MET cc_start: 0.8692 (mmt) cc_final: 0.8211 (mmt) REVERT: A 445 GLN cc_start: 0.8312 (pp30) cc_final: 0.7833 (pp30) REVERT: A 557 SER cc_start: 0.9015 (m) cc_final: 0.8649 (t) REVERT: A 606 ASN cc_start: 0.9209 (m-40) cc_final: 0.8821 (m110) REVERT: A 648 PHE cc_start: 0.9208 (p90) cc_final: 0.8954 (p90) REVERT: A 674 TYR cc_start: 0.8050 (m-80) cc_final: 0.7759 (m-10) REVERT: A 740 ASP cc_start: 0.6846 (m-30) cc_final: 0.6483 (m-30) REVERT: A 768 MET cc_start: 0.8242 (mtt) cc_final: 0.7953 (mtm) REVERT: A 783 LEU cc_start: 0.7877 (mm) cc_final: 0.7614 (mm) REVERT: D 84 ASP cc_start: 0.8126 (m-30) cc_final: 0.7526 (m-30) REVERT: D 228 ASN cc_start: 0.8366 (m110) cc_final: 0.8070 (m110) REVERT: E 31 ASP cc_start: 0.8499 (m-30) cc_final: 0.8107 (m-30) REVERT: E 101 LEU cc_start: 0.8447 (tp) cc_final: 0.8065 (tp) REVERT: E 104 ILE cc_start: 0.8760 (pt) cc_final: 0.8511 (mm) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.1828 time to fit residues: 51.9397 Evaluate side-chains 184 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 26 optimal weight: 0.3980 chunk 34 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 2 optimal weight: 50.0000 chunk 36 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 ASN A 731 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.154025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.099275 restraints weight = 40333.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.104553 restraints weight = 17588.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.107856 restraints weight = 11093.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.109878 restraints weight = 8625.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.110822 restraints weight = 7518.953| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.5335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7374 Z= 0.112 Angle : 0.504 7.167 9987 Z= 0.276 Chirality : 0.042 0.164 1046 Planarity : 0.004 0.063 1309 Dihedral : 4.146 17.812 1003 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.13 % Allowed : 0.53 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.27), residues: 879 helix: 1.05 (0.38), residues: 188 sheet: 0.17 (0.24), residues: 366 loop : 0.25 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 173 TYR 0.016 0.001 TYR A 653 PHE 0.025 0.001 PHE A 738 TRP 0.009 0.001 TRP A 576 HIS 0.001 0.000 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 7372) covalent geometry : angle 0.49967 ( 9983) SS BOND : bond 0.01171 ( 2) SS BOND : angle 3.40000 ( 4) hydrogen bonds : bond 0.03419 ( 394) hydrogen bonds : angle 5.19914 ( 1206) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.383 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: 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: 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: 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: P 1159 TYR cc_start: 0.6427 (t80) cc_final: 0.5890 (t80) REVERT: P 1270 ASP cc_start: 0.8575 (t70) cc_final: 0.8346 (t70) REVERT: P 1271 ASN cc_start: 0.8478 (p0) cc_final: 0.7946 (p0) REVERT: A 287 LEU cc_start: 0.9263 (pp) cc_final: 0.8783 (pp) REVERT: A 369 MET cc_start: 0.8699 (mmt) cc_final: 0.8273 (mmt) REVERT: A 422 ASN cc_start: 0.8001 (m-40) cc_final: 0.7640 (t0) REVERT: A 445 GLN cc_start: 0.8397 (pp30) cc_final: 0.7923 (pp30) REVERT: A 446 GLN cc_start: 0.8459 (mt0) cc_final: 0.7929 (mm-40) REVERT: A 557 SER cc_start: 0.9010 (m) cc_final: 0.8639 (t) REVERT: A 606 ASN cc_start: 0.9162 (m-40) cc_final: 0.8588 (m110) REVERT: A 630 LEU cc_start: 0.8589 (tp) cc_final: 0.8351 (tp) REVERT: A 709 ASN cc_start: 0.8552 (t160) cc_final: 0.7914 (t0) REVERT: D 84 ASP cc_start: 0.8115 (m-30) cc_final: 0.7511 (m-30) REVERT: D 187 GLU cc_start: 0.9019 (tp30) cc_final: 0.8676 (tp30) REVERT: D 228 ASN cc_start: 0.8285 (m110) cc_final: 0.7920 (m110) REVERT: E 31 ASP cc_start: 0.8446 (m-30) cc_final: 0.8058 (m-30) REVERT: E 78 ARG cc_start: 0.8324 (ttm-80) cc_final: 0.8041 (ttm-80) REVERT: E 101 LEU cc_start: 0.8564 (tp) cc_final: 0.8164 (tp) outliers start: 1 outliers final: 0 residues processed: 209 average time/residue: 0.1940 time to fit residues: 54.3201 Evaluate side-chains 181 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 30 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 10 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.154427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.103168 restraints weight = 40458.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.105825 restraints weight = 18169.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.107408 restraints weight = 12563.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.107970 restraints weight = 11625.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.108102 restraints weight = 10406.622| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.5540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7374 Z= 0.114 Angle : 0.493 6.232 9987 Z= 0.270 Chirality : 0.042 0.158 1046 Planarity : 0.004 0.044 1309 Dihedral : 4.074 18.500 1003 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.27), residues: 879 helix: 1.05 (0.38), residues: 190 sheet: 0.11 (0.24), residues: 369 loop : 0.22 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 173 TYR 0.014 0.001 TYR D 184 PHE 0.012 0.001 PHE A 572 TRP 0.010 0.001 TRP A 576 HIS 0.002 0.000 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 7372) covalent geometry : angle 0.48911 ( 9983) SS BOND : bond 0.00701 ( 2) SS BOND : angle 3.11553 ( 4) hydrogen bonds : bond 0.03284 ( 394) hydrogen bonds : angle 5.10049 ( 1206) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.411 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: 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: 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: 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: symmetry clash REVERT: P 1159 TYR cc_start: 0.6455 (t80) cc_final: 0.5937 (t80) REVERT: P 1270 ASP cc_start: 0.8756 (t70) cc_final: 0.8524 (t70) REVERT: P 1271 ASN cc_start: 0.8588 (p0) cc_final: 0.8056 (p0) REVERT: A 284 ILE cc_start: 0.9195 (mm) cc_final: 0.8726 (tp) REVERT: A 287 LEU cc_start: 0.9094 (pp) cc_final: 0.8767 (pp) REVERT: A 369 MET cc_start: 0.8583 (mmt) cc_final: 0.8252 (mmt) REVERT: A 422 ASN cc_start: 0.8128 (m-40) cc_final: 0.7811 (t0) REVERT: A 445 GLN cc_start: 0.8371 (pp30) cc_final: 0.7946 (pp30) REVERT: A 446 GLN cc_start: 0.8439 (mt0) cc_final: 0.7952 (mm-40) REVERT: A 557 SER cc_start: 0.8991 (m) cc_final: 0.8614 (t) REVERT: A 606 ASN cc_start: 0.9252 (m-40) cc_final: 0.8687 (m110) REVERT: A 630 LEU cc_start: 0.8685 (tp) cc_final: 0.8423 (tp) REVERT: A 740 ASP cc_start: 0.6597 (m-30) cc_final: 0.6357 (m-30) REVERT: A 783 LEU cc_start: 0.7892 (mm) cc_final: 0.7681 (mm) REVERT: D 84 ASP cc_start: 0.7930 (m-30) cc_final: 0.7354 (m-30) REVERT: D 127 PHE cc_start: 0.8656 (t80) cc_final: 0.8425 (t80) REVERT: D 228 ASN cc_start: 0.8299 (m110) cc_final: 0.7921 (m110) REVERT: E 31 ASP cc_start: 0.8433 (m-30) cc_final: 0.8039 (m-30) REVERT: E 101 LEU cc_start: 0.8614 (tp) cc_final: 0.8387 (tp) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.1743 time to fit residues: 48.6016 Evaluate side-chains 182 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 87 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 80 optimal weight: 0.4980 chunk 1 optimal weight: 50.0000 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 = 0.3996 r_free = 0.3996 target = 0.152826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.101890 restraints weight = 40553.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.104727 restraints weight = 18176.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.105696 restraints weight = 12325.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.106777 restraints weight = 11610.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.106660 restraints weight = 10430.668| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.5756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7374 Z= 0.144 Angle : 0.498 5.068 9987 Z= 0.276 Chirality : 0.042 0.160 1046 Planarity : 0.004 0.069 1309 Dihedral : 4.080 19.833 1003 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.27), residues: 879 helix: 0.99 (0.38), residues: 190 sheet: -0.01 (0.24), residues: 369 loop : 0.12 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 173 TYR 0.015 0.001 TYR D 184 PHE 0.013 0.001 PHE A 572 TRP 0.009 0.001 TRP A 576 HIS 0.003 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 7372) covalent geometry : angle 0.49537 ( 9983) SS BOND : bond 0.00688 ( 2) SS BOND : angle 2.69240 ( 4) hydrogen bonds : bond 0.03296 ( 394) hydrogen bonds : angle 5.07530 ( 1206) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.414 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: 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: 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: 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: symmetry clash REVERT: P 1159 TYR cc_start: 0.6450 (t80) cc_final: 0.5983 (t80) REVERT: P 1270 ASP cc_start: 0.8713 (t70) cc_final: 0.8407 (t0) REVERT: P 1271 ASN cc_start: 0.8544 (p0) cc_final: 0.8123 (p0) REVERT: A 284 ILE cc_start: 0.9198 (mm) cc_final: 0.8739 (tp) REVERT: A 307 ASP cc_start: 0.8386 (t70) cc_final: 0.8059 (t0) REVERT: A 371 GLN cc_start: 0.8327 (tp40) cc_final: 0.7998 (tp-100) REVERT: A 422 ASN cc_start: 0.8126 (m-40) cc_final: 0.7801 (t0) REVERT: A 446 GLN cc_start: 0.8406 (mt0) cc_final: 0.8046 (mm-40) REVERT: A 557 SER cc_start: 0.9043 (m) cc_final: 0.8655 (t) REVERT: A 630 LEU cc_start: 0.8738 (tp) cc_final: 0.8478 (tp) REVERT: A 666 ASN cc_start: 0.9009 (m-40) cc_final: 0.8808 (t0) REVERT: A 740 ASP cc_start: 0.6595 (m-30) cc_final: 0.6329 (m-30) REVERT: A 783 LEU cc_start: 0.7901 (mm) cc_final: 0.7689 (mm) REVERT: D 84 ASP cc_start: 0.7995 (m-30) cc_final: 0.7418 (m-30) REVERT: D 132 ARG cc_start: 0.8370 (mmm-85) cc_final: 0.7632 (mmm-85) REVERT: D 228 ASN cc_start: 0.8299 (m110) cc_final: 0.7935 (m110) REVERT: E 31 ASP cc_start: 0.8484 (m-30) cc_final: 0.8095 (m-30) REVERT: E 101 LEU cc_start: 0.8628 (tp) cc_final: 0.8303 (tp) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.1744 time to fit residues: 49.2660 Evaluate side-chains 180 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 0.2980 chunk 7 optimal weight: 20.0000 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 226 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.151906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.099827 restraints weight = 41364.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.102180 restraints weight = 18684.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.103047 restraints weight = 12679.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.103782 restraints weight = 12374.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.103915 restraints weight = 10906.352| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.5970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7374 Z= 0.171 Angle : 0.514 4.920 9987 Z= 0.286 Chirality : 0.042 0.176 1046 Planarity : 0.004 0.062 1309 Dihedral : 4.137 17.518 1003 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.27), residues: 879 helix: 0.87 (0.38), residues: 190 sheet: -0.12 (0.24), residues: 380 loop : -0.01 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 173 TYR 0.016 0.001 TYR D 184 PHE 0.012 0.001 PHE A 738 TRP 0.009 0.001 TRP A 576 HIS 0.021 0.002 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 7372) covalent geometry : angle 0.51105 ( 9983) SS BOND : bond 0.00589 ( 2) SS BOND : angle 2.62366 ( 4) hydrogen bonds : bond 0.03402 ( 394) hydrogen bonds : angle 5.16288 ( 1206) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.393 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: 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: 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: 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: symmetry clash REVERT: P 1159 TYR cc_start: 0.6454 (t80) cc_final: 0.6040 (t80) REVERT: P 1270 ASP cc_start: 0.8842 (t70) cc_final: 0.8441 (t0) REVERT: P 1271 ASN cc_start: 0.8761 (p0) cc_final: 0.8318 (p0) REVERT: A 284 ILE cc_start: 0.9188 (mm) cc_final: 0.8665 (tp) REVERT: A 307 ASP cc_start: 0.8457 (t70) cc_final: 0.8118 (t0) REVERT: A 422 ASN cc_start: 0.8181 (m-40) cc_final: 0.7861 (t0) REVERT: A 445 GLN cc_start: 0.8461 (pp30) cc_final: 0.8173 (pp30) REVERT: A 557 SER cc_start: 0.9005 (m) cc_final: 0.8640 (t) REVERT: A 606 ASN cc_start: 0.9273 (m-40) cc_final: 0.8853 (m110) REVERT: A 630 LEU cc_start: 0.8725 (tp) cc_final: 0.8447 (tp) REVERT: A 666 ASN cc_start: 0.9092 (m-40) cc_final: 0.8859 (t0) REVERT: A 740 ASP cc_start: 0.6734 (m-30) cc_final: 0.6458 (m-30) REVERT: A 783 LEU cc_start: 0.7976 (mm) cc_final: 0.7726 (mm) REVERT: D 84 ASP cc_start: 0.7928 (m-30) cc_final: 0.7350 (m-30) REVERT: D 127 PHE cc_start: 0.8641 (t80) cc_final: 0.8413 (t80) REVERT: D 132 ARG cc_start: 0.8382 (mmm-85) cc_final: 0.7560 (mmm-85) REVERT: D 228 ASN cc_start: 0.8424 (m110) cc_final: 0.7974 (m110) REVERT: E 31 ASP cc_start: 0.8596 (m-30) cc_final: 0.8167 (m-30) REVERT: E 101 LEU cc_start: 0.8711 (tp) cc_final: 0.8377 (tp) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1965 time to fit residues: 54.1755 Evaluate side-chains 177 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 4 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 226 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.151642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.097146 restraints weight = 40748.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.102129 restraints weight = 18719.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.105244 restraints weight = 12130.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.107155 restraints weight = 9512.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.108065 restraints weight = 8331.280| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.6033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7374 Z= 0.162 Angle : 0.516 5.169 9987 Z= 0.286 Chirality : 0.042 0.169 1046 Planarity : 0.005 0.098 1309 Dihedral : 4.161 20.463 1003 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.27), residues: 879 helix: 0.81 (0.38), residues: 190 sheet: -0.12 (0.24), residues: 374 loop : -0.09 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 421 TYR 0.033 0.001 TYR A 585 PHE 0.021 0.001 PHE A 586 TRP 0.009 0.001 TRP A 576 HIS 0.015 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 7372) covalent geometry : angle 0.51303 ( 9983) SS BOND : bond 0.00482 ( 2) SS BOND : angle 2.61343 ( 4) hydrogen bonds : bond 0.03354 ( 394) hydrogen bonds : angle 5.18099 ( 1206) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.424 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: 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: 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: 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: symmetry clash revert: symmetry clash REVERT: P 1159 TYR cc_start: 0.6432 (t80) cc_final: 0.5985 (t80) REVERT: P 1270 ASP cc_start: 0.8620 (t70) cc_final: 0.8209 (t0) REVERT: P 1271 ASN cc_start: 0.8627 (p0) cc_final: 0.8228 (p0) REVERT: A 284 ILE cc_start: 0.9191 (mm) cc_final: 0.8584 (tp) REVERT: A 307 ASP cc_start: 0.8383 (t70) cc_final: 0.8076 (t0) REVERT: A 445 GLN cc_start: 0.8557 (pp30) cc_final: 0.8272 (pp30) REVERT: A 557 SER cc_start: 0.9016 (m) cc_final: 0.8657 (t) REVERT: A 606 ASN cc_start: 0.9188 (m-40) cc_final: 0.8780 (m110) REVERT: A 630 LEU cc_start: 0.8720 (tp) cc_final: 0.8459 (tp) REVERT: A 666 ASN cc_start: 0.9125 (m-40) cc_final: 0.8900 (t0) REVERT: A 740 ASP cc_start: 0.6623 (m-30) cc_final: 0.6315 (m-30) REVERT: A 783 LEU cc_start: 0.7924 (mm) cc_final: 0.7712 (mm) REVERT: D 84 ASP cc_start: 0.8129 (m-30) cc_final: 0.7515 (m-30) REVERT: D 132 ARG cc_start: 0.8405 (mmm-85) cc_final: 0.7548 (mtp85) REVERT: D 232 GLU cc_start: 0.8528 (mp0) cc_final: 0.8223 (mp0) REVERT: E 31 ASP cc_start: 0.8626 (m-30) cc_final: 0.8194 (m-30) REVERT: E 101 LEU cc_start: 0.8473 (tp) cc_final: 0.8061 (tp) REVERT: E 104 ILE cc_start: 0.8783 (pt) cc_final: 0.8500 (mm) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.1952 time to fit residues: 52.4606 Evaluate side-chains 176 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 79 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 1 optimal weight: 90.0000 chunk 19 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3999 r_free = 0.3999 target = 0.153259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.101599 restraints weight = 41164.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.104222 restraints weight = 18641.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.105032 restraints weight = 12867.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.105810 restraints weight = 12447.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.105943 restraints weight = 11059.266| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.6135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7374 Z= 0.107 Angle : 0.482 5.229 9987 Z= 0.265 Chirality : 0.042 0.169 1046 Planarity : 0.004 0.066 1309 Dihedral : 4.014 20.019 1003 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.28), residues: 879 helix: 1.03 (0.39), residues: 190 sheet: -0.02 (0.24), residues: 371 loop : -0.05 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 173 TYR 0.020 0.001 TYR A 585 PHE 0.011 0.001 PHE A 572 TRP 0.010 0.001 TRP A 576 HIS 0.012 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 7372) covalent geometry : angle 0.48010 ( 9983) SS BOND : bond 0.00440 ( 2) SS BOND : angle 2.40114 ( 4) hydrogen bonds : bond 0.03089 ( 394) hydrogen bonds : angle 4.99574 ( 1206) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.346 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1159 TYR cc_start: 0.6473 (t80) cc_final: 0.6025 (t80) REVERT: P 1270 ASP cc_start: 0.8803 (t70) cc_final: 0.8334 (t0) REVERT: P 1271 ASN cc_start: 0.8729 (p0) cc_final: 0.8311 (p0) REVERT: A 284 ILE cc_start: 0.9168 (mm) cc_final: 0.8634 (tp) REVERT: A 307 ASP cc_start: 0.8386 (t70) cc_final: 0.8052 (t0) REVERT: A 445 GLN cc_start: 0.8534 (pp30) cc_final: 0.8235 (pp30) REVERT: A 557 SER cc_start: 0.9023 (m) cc_final: 0.8651 (t) REVERT: A 606 ASN cc_start: 0.9185 (m-40) cc_final: 0.8758 (m110) REVERT: A 630 LEU cc_start: 0.8695 (tp) cc_final: 0.8416 (tp) REVERT: D 84 ASP cc_start: 0.7993 (m-30) cc_final: 0.7381 (m-30) REVERT: D 127 PHE cc_start: 0.8542 (t80) cc_final: 0.8317 (t80) REVERT: D 232 GLU cc_start: 0.8667 (mp0) cc_final: 0.8334 (mp0) REVERT: E 31 ASP cc_start: 0.8536 (m-30) cc_final: 0.8117 (m-30) REVERT: E 101 LEU cc_start: 0.8615 (tp) cc_final: 0.8276 (tp) REVERT: E 104 ILE cc_start: 0.8871 (pt) cc_final: 0.8591 (mm) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1877 time to fit residues: 50.6496 Evaluate side-chains 180 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 29 optimal weight: 0.3980 chunk 39 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.152769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.100573 restraints weight = 41566.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.102865 restraints weight = 19400.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.103779 restraints weight = 13681.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.104491 restraints weight = 13150.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.104766 restraints weight = 11778.132| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.6257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7374 Z= 0.155 Angle : 0.503 5.011 9987 Z= 0.279 Chirality : 0.042 0.165 1046 Planarity : 0.004 0.068 1309 Dihedral : 4.056 18.116 1003 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.27), residues: 879 helix: 0.85 (0.38), residues: 190 sheet: -0.10 (0.24), residues: 373 loop : -0.14 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 173 TYR 0.019 0.001 TYR C 65 PHE 0.013 0.001 PHE P1278 TRP 0.008 0.001 TRP A 635 HIS 0.013 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 7372) covalent geometry : angle 0.50030 ( 9983) SS BOND : bond 0.00508 ( 2) SS BOND : angle 2.50358 ( 4) hydrogen bonds : bond 0.03285 ( 394) hydrogen bonds : angle 5.07496 ( 1206) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2805.32 seconds wall clock time: 48 minutes 27.38 seconds (2907.38 seconds total)