Starting phenix.real_space_refine on Thu Jun 12 17:28:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tt6_26112/06_2025/7tt6_26112.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tt6_26112/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7tt6_26112/06_2025/7tt6_26112.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tt6_26112/06_2025/7tt6_26112.map" model { file = "/net/cci-nas-00/data/ceres_data/7tt6_26112/06_2025/7tt6_26112.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tt6_26112/06_2025/7tt6_26112.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.95, per 1000 atoms: 0.49 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: 3.31 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.16 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: 4.87 Time building geometry restraints manager: 4.09 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: 1.060 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: 0.210 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 30.990 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.950 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.018 0.002 TRP A 449 HIS 0.008 0.003 HIS A 555 PHE 0.016 0.002 PHE A 791 TYR 0.023 0.002 TYR A 585 ARG 0.011 0.001 ARG D 135 Details of bonding type rmsd hydrogen bonds : bond 0.12900 ( 394) hydrogen bonds : angle 7.73821 ( 1206) SS BOND : bond 0.00395 ( 2) SS BOND : angle 3.87000 ( 4) covalent geometry : bond 0.00483 ( 7372) covalent geometry : angle 0.90963 ( 9983) *********************** 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 : 1.134 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 1260 MET cc_start: 0.4627 (mtm) cc_final: 0.4335 (mpp) REVERT: A 307 ASP cc_start: 0.8373 (m-30) cc_final: 0.8078 (m-30) REVERT: A 422 ASN cc_start: 0.7854 (m-40) cc_final: 0.7568 (m-40) REVERT: A 542 GLN cc_start: 0.8887 (mt0) cc_final: 0.8669 (mm-40) REVERT: A 557 SER cc_start: 0.8992 (m) cc_final: 0.8619 (t) REVERT: A 633 THR cc_start: 0.8382 (p) cc_final: 0.8109 (p) REVERT: A 768 MET cc_start: 0.7980 (mtt) cc_final: 0.7521 (mtm) REVERT: A 783 LEU cc_start: 0.7923 (mt) cc_final: 0.7723 (mt) 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: 0.8460 (t80) REVERT: D 208 THR cc_start: 0.9142 (t) cc_final: 0.8911 (t) REVERT: D 228 ASN cc_start: 0.8670 (m-40) cc_final: 0.8309 (m-40) REVERT: E 31 ASP cc_start: 0.8285 (m-30) cc_final: 0.7616 (p0) REVERT: E 41 ASN cc_start: 0.9062 (m-40) cc_final: 0.8727 (t0) REVERT: E 43 VAL cc_start: 0.9383 (t) cc_final: 0.9142 (t) REVERT: E 64 MET cc_start: 0.8471 (mtp) cc_final: 0.8247 (mtm) REVERT: E 80 GLN cc_start: 0.8626 (tp40) cc_final: 0.8297 (tp40) REVERT: E 81 PRO cc_start: 0.8877 (Cg_exo) cc_final: 0.8384 (Cg_endo) REVERT: E 95 PHE cc_start: 0.8396 (m-80) cc_final: 0.8146 (m-80) REVERT: E 103 ASN cc_start: 0.9095 (t0) cc_final: 0.8782 (t0) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.4533 time to fit residues: 174.3317 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 : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 D 241 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.154914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.099590 restraints weight = 40458.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.105150 restraints weight = 17587.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.108604 restraints weight = 11026.835| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7374 Z= 0.169 Angle : 0.597 6.665 9987 Z= 0.339 Chirality : 0.044 0.182 1046 Planarity : 0.004 0.040 1309 Dihedral : 4.676 38.320 1003 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.27 % Allowed : 1.20 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.27), residues: 879 helix: 0.31 (0.36), residues: 187 sheet: 0.69 (0.24), residues: 373 loop : 0.51 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 576 HIS 0.004 0.001 HIS C 51 PHE 0.014 0.001 PHE P1300 TYR 0.019 0.001 TYR D 184 ARG 0.005 0.001 ARG D 212 Details of bonding type rmsd hydrogen bonds : bond 0.04831 ( 394) hydrogen bonds : angle 6.18594 ( 1206) SS BOND : bond 0.00831 ( 2) SS BOND : angle 4.47753 ( 4) covalent geometry : bond 0.00355 ( 7372) covalent geometry : angle 0.58987 ( 9983) *********************** 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 233 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 231 time to evaluate : 1.194 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: P 1119 ILE cc_start: 0.8781 (mt) cc_final: 0.8548 (tp) REVERT: P 1271 ASN cc_start: 0.8490 (p0) cc_final: 0.7737 (p0) REVERT: P 1292 VAL cc_start: 0.8199 (p) cc_final: 0.7817 (m) REVERT: A 288 THR cc_start: 0.9210 (m) cc_final: 0.8901 (p) REVERT: A 369 MET cc_start: 0.8742 (mmt) cc_final: 0.8197 (mmt) REVERT: A 422 ASN cc_start: 0.8305 (m-40) cc_final: 0.8045 (m-40) REVERT: A 426 PHE cc_start: 0.8810 (t80) cc_final: 0.8526 (t80) REVERT: A 445 GLN cc_start: 0.8316 (pp30) cc_final: 0.7738 (pm20) REVERT: A 446 GLN cc_start: 0.8688 (mt0) cc_final: 0.8398 (mt0) REVERT: A 542 GLN cc_start: 0.9004 (mt0) cc_final: 0.8668 (mm-40) REVERT: A 557 SER cc_start: 0.8993 (m) cc_final: 0.8627 (t) REVERT: A 727 ASP cc_start: 0.8985 (p0) cc_final: 0.8663 (p0) REVERT: A 768 MET cc_start: 0.8212 (mtt) cc_final: 0.7878 (mtm) REVERT: D 84 ASP cc_start: 0.8045 (m-30) cc_final: 0.7541 (m-30) REVERT: D 127 PHE cc_start: 0.8678 (t80) cc_final: 0.8476 (t80) REVERT: D 207 ASP cc_start: 0.7983 (m-30) cc_final: 0.7173 (m-30) REVERT: E 31 ASP cc_start: 0.8356 (m-30) cc_final: 0.8119 (m-30) REVERT: E 41 ASN cc_start: 0.9116 (m-40) cc_final: 0.8683 (t0) outliers start: 2 outliers final: 0 residues processed: 231 average time/residue: 0.4367 time to fit residues: 132.2746 Evaluate side-chains 197 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 46 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 79 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 59 optimal weight: 0.0670 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 68 optimal weight: 8.9990 overall best weight: 1.4522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.153818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.097563 restraints weight = 41123.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.102763 restraints weight = 18326.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.105993 restraints weight = 11809.277| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7374 Z= 0.172 Angle : 0.547 4.824 9987 Z= 0.309 Chirality : 0.043 0.173 1046 Planarity : 0.005 0.065 1309 Dihedral : 4.390 21.127 1003 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.27), residues: 879 helix: 0.72 (0.36), residues: 187 sheet: 0.36 (0.24), residues: 372 loop : 0.51 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 576 HIS 0.002 0.001 HIS A 533 PHE 0.013 0.001 PHE A 570 TYR 0.016 0.001 TYR D 184 ARG 0.007 0.001 ARG A 734 Details of bonding type rmsd hydrogen bonds : bond 0.04138 ( 394) hydrogen bonds : angle 5.72649 ( 1206) SS BOND : bond 0.00613 ( 2) SS BOND : angle 2.89544 ( 4) covalent geometry : bond 0.00357 ( 7372) covalent geometry : angle 0.54405 ( 9983) *********************** 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 214 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 1.088 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: P 1271 ASN cc_start: 0.8378 (p0) cc_final: 0.7808 (p0) REVERT: A 369 MET cc_start: 0.8695 (mmt) cc_final: 0.8137 (mmt) REVERT: A 422 ASN cc_start: 0.8321 (m-40) cc_final: 0.7899 (m-40) REVERT: A 445 GLN cc_start: 0.8371 (pp30) cc_final: 0.7792 (pm20) REVERT: A 446 GLN cc_start: 0.8643 (mt0) cc_final: 0.8299 (mt0) REVERT: A 557 SER cc_start: 0.8952 (m) cc_final: 0.8546 (t) REVERT: A 648 PHE cc_start: 0.9203 (p90) cc_final: 0.8980 (p90) REVERT: A 768 MET cc_start: 0.8240 (mtt) cc_final: 0.7950 (mtm) REVERT: D 84 ASP cc_start: 0.8042 (m-30) cc_final: 0.7498 (m-30) REVERT: D 127 PHE cc_start: 0.8679 (t80) cc_final: 0.8457 (t80) REVERT: D 136 ASP cc_start: 0.9341 (t0) cc_final: 0.9132 (t0) REVERT: D 228 ASN cc_start: 0.8435 (m110) cc_final: 0.8047 (m110) REVERT: E 31 ASP cc_start: 0.8401 (m-30) cc_final: 0.8082 (m-30) REVERT: E 41 ASN cc_start: 0.9107 (m-40) cc_final: 0.8725 (t0) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.4090 time to fit residues: 115.8150 Evaluate side-chains 191 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 52 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 69 optimal weight: 0.1980 chunk 65 optimal weight: 0.0030 chunk 87 optimal weight: 1.9990 chunk 66 optimal weight: 0.0970 chunk 41 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 4 optimal weight: 30.0000 overall best weight: 0.6390 ------------------------------------------------------------------------------- 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 = 0.4017 r_free = 0.4017 target = 0.155464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.100298 restraints weight = 40332.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.105487 restraints weight = 18363.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.108759 restraints weight = 11856.578| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7374 Z= 0.107 Angle : 0.515 10.287 9987 Z= 0.284 Chirality : 0.042 0.172 1046 Planarity : 0.004 0.041 1309 Dihedral : 4.232 20.825 1003 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.27), residues: 879 helix: 1.00 (0.38), residues: 187 sheet: 0.25 (0.24), residues: 375 loop : 0.45 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 576 HIS 0.009 0.001 HIS A 533 PHE 0.010 0.001 PHE D 144 TYR 0.016 0.001 TYR P1298 ARG 0.003 0.000 ARG P1269 Details of bonding type rmsd hydrogen bonds : bond 0.03655 ( 394) hydrogen bonds : angle 5.41806 ( 1206) SS BOND : bond 0.00435 ( 2) SS BOND : angle 3.89024 ( 4) covalent geometry : bond 0.00221 ( 7372) covalent geometry : angle 0.50917 ( 9983) *********************** 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 : 1.085 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 1270 ASP cc_start: 0.8670 (t70) cc_final: 0.8373 (t0) REVERT: P 1271 ASN cc_start: 0.8569 (p0) cc_final: 0.8179 (p0) REVERT: P 1278 PHE cc_start: 0.6711 (t80) cc_final: 0.6419 (t80) REVERT: P 1279 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8251 (tm-30) REVERT: A 369 MET cc_start: 0.8699 (mmt) cc_final: 0.8191 (mmt) REVERT: A 445 GLN cc_start: 0.8271 (pp30) cc_final: 0.7801 (pm20) REVERT: A 446 GLN cc_start: 0.8740 (mt0) cc_final: 0.8519 (mt0) REVERT: A 557 SER cc_start: 0.8939 (m) cc_final: 0.8531 (t) REVERT: A 648 PHE cc_start: 0.9182 (p90) cc_final: 0.8949 (p90) REVERT: A 740 ASP cc_start: 0.6703 (m-30) cc_final: 0.6338 (m-30) REVERT: A 768 MET cc_start: 0.8228 (mtt) cc_final: 0.7990 (mtm) REVERT: A 783 LEU cc_start: 0.7918 (mm) cc_final: 0.7705 (mm) REVERT: D 84 ASP cc_start: 0.8086 (m-30) cc_final: 0.7494 (m-30) REVERT: D 127 PHE cc_start: 0.8684 (t80) cc_final: 0.8464 (t80) REVERT: E 31 ASP cc_start: 0.8383 (m-30) cc_final: 0.8040 (m-30) REVERT: E 104 ILE cc_start: 0.8777 (pt) cc_final: 0.8539 (mm) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.4411 time to fit residues: 127.5835 Evaluate side-chains 188 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 52 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 16 optimal weight: 0.2980 chunk 59 optimal weight: 5.9990 chunk 13 optimal weight: 20.0000 chunk 83 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.151689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.096948 restraints weight = 40528.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.102010 restraints weight = 18505.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.105095 restraints weight = 11955.398| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.5321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7374 Z= 0.177 Angle : 0.539 6.336 9987 Z= 0.302 Chirality : 0.042 0.165 1046 Planarity : 0.005 0.071 1309 Dihedral : 4.302 19.351 1003 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.27), residues: 879 helix: 0.76 (0.38), residues: 189 sheet: 0.11 (0.24), residues: 363 loop : 0.06 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 576 HIS 0.006 0.001 HIS A 533 PHE 0.025 0.001 PHE A 738 TYR 0.016 0.001 TYR D 184 ARG 0.004 0.001 ARG D 173 Details of bonding type rmsd hydrogen bonds : bond 0.03688 ( 394) hydrogen bonds : angle 5.39185 ( 1206) SS BOND : bond 0.00882 ( 2) SS BOND : angle 3.28608 ( 4) covalent geometry : bond 0.00373 ( 7372) covalent geometry : angle 0.53522 ( 9983) *********************** 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 208 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 1.049 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: 0.6219 (t80) cc_final: 0.5900 (t80) REVERT: P 1270 ASP cc_start: 0.8710 (t70) cc_final: 0.8387 (t70) REVERT: P 1271 ASN cc_start: 0.8522 (p0) cc_final: 0.8183 (p0) REVERT: A 284 ILE cc_start: 0.9242 (mm) cc_final: 0.8686 (tp) REVERT: A 307 ASP cc_start: 0.8444 (t70) cc_final: 0.8119 (t0) REVERT: A 445 GLN cc_start: 0.8339 (pp30) cc_final: 0.7727 (pm20) REVERT: A 557 SER cc_start: 0.9010 (m) cc_final: 0.8597 (t) REVERT: A 630 LEU cc_start: 0.8638 (tp) cc_final: 0.8351 (tp) REVERT: A 709 ASN cc_start: 0.8672 (t0) cc_final: 0.8067 (t0) REVERT: A 783 LEU cc_start: 0.7910 (mm) cc_final: 0.7579 (mm) REVERT: D 84 ASP cc_start: 0.8092 (m-30) cc_final: 0.7483 (m-30) REVERT: D 196 ASN cc_start: 0.8975 (m-40) cc_final: 0.8529 (t0) REVERT: E 31 ASP cc_start: 0.8510 (m-30) cc_final: 0.7785 (p0) REVERT: E 104 ILE cc_start: 0.8737 (pt) cc_final: 0.8480 (mm) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.3881 time to fit residues: 108.3218 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 : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 73 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 4 optimal weight: 40.0000 chunk 25 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN A 446 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.153242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.097046 restraints weight = 41188.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.102346 restraints weight = 18256.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.105613 restraints weight = 11699.220| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.5580 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= 0.128 Angle : 0.498 5.168 9987 Z= 0.276 Chirality : 0.042 0.156 1046 Planarity : 0.004 0.059 1309 Dihedral : 4.165 19.820 1003 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.27), residues: 879 helix: 0.91 (0.38), residues: 190 sheet: -0.01 (0.23), residues: 374 loop : 0.04 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 576 HIS 0.003 0.001 HIS A 533 PHE 0.007 0.001 PHE E 77 TYR 0.014 0.001 TYR D 184 ARG 0.006 0.000 ARG D 173 Details of bonding type rmsd hydrogen bonds : bond 0.03383 ( 394) hydrogen bonds : angle 5.17077 ( 1206) SS BOND : bond 0.00778 ( 2) SS BOND : angle 3.05278 ( 4) covalent geometry : bond 0.00269 ( 7372) covalent geometry : angle 0.49451 ( 9983) *********************** 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 213 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 1.134 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: symmetry clash revert: symmetry clash REVERT: P 1159 TYR cc_start: 0.6338 (t80) cc_final: 0.5915 (t80) REVERT: P 1270 ASP cc_start: 0.8649 (t70) cc_final: 0.8364 (t0) REVERT: P 1271 ASN cc_start: 0.8516 (p0) cc_final: 0.8137 (p0) REVERT: A 284 ILE cc_start: 0.9240 (mm) cc_final: 0.8592 (tp) REVERT: A 307 ASP cc_start: 0.8388 (t70) cc_final: 0.8080 (t0) REVERT: A 369 MET cc_start: 0.8782 (mmt) cc_final: 0.8348 (mmt) REVERT: A 386 LYS cc_start: 0.8987 (mttm) cc_final: 0.8749 (mttm) REVERT: A 445 GLN cc_start: 0.8449 (pp30) cc_final: 0.8011 (pp30) REVERT: A 557 SER cc_start: 0.9005 (m) cc_final: 0.8597 (t) REVERT: A 630 LEU cc_start: 0.8651 (tp) cc_final: 0.8367 (tp) REVERT: A 740 ASP cc_start: 0.6740 (m-30) cc_final: 0.6459 (m-30) REVERT: D 84 ASP cc_start: 0.7969 (m-30) cc_final: 0.7362 (m-30) REVERT: D 136 ASP cc_start: 0.9394 (t0) cc_final: 0.9166 (t0) REVERT: E 31 ASP cc_start: 0.8446 (m-30) cc_final: 0.8094 (m-30) REVERT: E 104 ILE cc_start: 0.8798 (pt) cc_final: 0.8586 (mm) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.3980 time to fit residues: 113.6590 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 : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 78 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 8 optimal weight: 30.0000 chunk 1 optimal weight: 40.0000 chunk 40 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN A 709 ASN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.150576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.096063 restraints weight = 40722.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.100967 restraints weight = 18663.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.104015 restraints weight = 12136.693| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.5813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7374 Z= 0.182 Angle : 0.523 4.745 9987 Z= 0.293 Chirality : 0.042 0.152 1046 Planarity : 0.004 0.055 1309 Dihedral : 4.262 17.812 1003 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.13 % Allowed : 0.80 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.27), residues: 879 helix: 0.77 (0.38), residues: 190 sheet: -0.12 (0.24), residues: 369 loop : -0.13 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 576 HIS 0.003 0.001 HIS A 533 PHE 0.014 0.001 PHE P1278 TYR 0.015 0.001 TYR D 184 ARG 0.007 0.001 ARG D 173 Details of bonding type rmsd hydrogen bonds : bond 0.03539 ( 394) hydrogen bonds : angle 5.26782 ( 1206) SS BOND : bond 0.00839 ( 2) SS BOND : angle 3.14541 ( 4) covalent geometry : bond 0.00387 ( 7372) covalent geometry : angle 0.51957 ( 9983) *********************** 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: 1 poor density : 207 time to evaluate : 1.029 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: 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: 0.6028 (t80) REVERT: P 1270 ASP cc_start: 0.8629 (t70) cc_final: 0.8280 (t0) REVERT: P 1271 ASN cc_start: 0.8547 (p0) cc_final: 0.8147 (p0) REVERT: A 284 ILE cc_start: 0.9228 (mm) cc_final: 0.8557 (tp) REVERT: A 307 ASP cc_start: 0.8442 (t70) cc_final: 0.8150 (t0) REVERT: A 445 GLN cc_start: 0.8472 (pp30) cc_final: 0.7777 (pm20) REVERT: A 557 SER cc_start: 0.9066 (m) cc_final: 0.8677 (t) REVERT: A 630 LEU cc_start: 0.8698 (tp) cc_final: 0.8429 (tp) REVERT: A 740 ASP cc_start: 0.6783 (m-30) cc_final: 0.6493 (m-30) REVERT: A 783 LEU cc_start: 0.7932 (mm) cc_final: 0.7731 (mm) REVERT: D 84 ASP cc_start: 0.7986 (m-30) cc_final: 0.7383 (m-30) REVERT: D 132 ARG cc_start: 0.8421 (mmm-85) cc_final: 0.7682 (mmm-85) REVERT: D 196 ASN cc_start: 0.9056 (m-40) cc_final: 0.8543 (t0) REVERT: E 31 ASP cc_start: 0.8559 (m-30) cc_final: 0.8178 (m-30) REVERT: E 104 ILE cc_start: 0.8803 (pt) cc_final: 0.8579 (mm) outliers start: 1 outliers final: 0 residues processed: 207 average time/residue: 0.4304 time to fit residues: 117.9978 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 : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 0 optimal weight: 80.0000 chunk 42 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN A 534 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.153005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.097174 restraints weight = 40757.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.102347 restraints weight = 18100.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.105684 restraints weight = 11649.481| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.6018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7374 Z= 0.111 Angle : 0.486 5.258 9987 Z= 0.267 Chirality : 0.042 0.180 1046 Planarity : 0.004 0.066 1309 Dihedral : 4.129 20.948 1003 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.27), residues: 879 helix: 1.03 (0.39), residues: 190 sheet: 0.04 (0.24), residues: 368 loop : -0.13 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 576 HIS 0.002 0.000 HIS A 533 PHE 0.012 0.001 PHE E 77 TYR 0.012 0.001 TYR D 184 ARG 0.006 0.000 ARG D 173 Details of bonding type rmsd hydrogen bonds : bond 0.03169 ( 394) hydrogen bonds : angle 5.01717 ( 1206) SS BOND : bond 0.00588 ( 2) SS BOND : angle 3.83031 ( 4) covalent geometry : bond 0.00236 ( 7372) covalent geometry : angle 0.48020 ( 9983) *********************** 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 205 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 1.057 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: P 1159 TYR cc_start: 0.6453 (t80) cc_final: 0.6011 (t80) REVERT: P 1270 ASP cc_start: 0.8676 (t70) cc_final: 0.8294 (t0) REVERT: P 1271 ASN cc_start: 0.8605 (p0) cc_final: 0.8286 (p0) REVERT: A 284 ILE cc_start: 0.9217 (mm) cc_final: 0.8551 (tp) REVERT: A 307 ASP cc_start: 0.8401 (t70) cc_final: 0.8106 (t0) REVERT: A 445 GLN cc_start: 0.8498 (pp30) cc_final: 0.7792 (pm20) REVERT: A 557 SER cc_start: 0.9080 (m) cc_final: 0.8696 (t) REVERT: A 630 LEU cc_start: 0.8695 (tp) cc_final: 0.8413 (tp) REVERT: A 666 ASN cc_start: 0.9265 (m-40) cc_final: 0.8970 (m-40) REVERT: A 740 ASP cc_start: 0.6664 (m-30) cc_final: 0.6395 (m-30) REVERT: A 783 LEU cc_start: 0.7932 (mm) cc_final: 0.7705 (mm) REVERT: A 791 PHE cc_start: 0.8425 (m-80) cc_final: 0.8220 (m-10) REVERT: D 84 ASP cc_start: 0.8056 (m-30) cc_final: 0.7453 (m-30) REVERT: D 132 ARG cc_start: 0.8408 (mmm-85) cc_final: 0.7605 (mtp85) REVERT: D 136 ASP cc_start: 0.9377 (t0) cc_final: 0.9163 (t0) REVERT: D 187 GLU cc_start: 0.8999 (tp30) cc_final: 0.8719 (tp30) REVERT: E 31 ASP cc_start: 0.8432 (m-30) cc_final: 0.8043 (m-30) REVERT: E 104 ILE cc_start: 0.8799 (pt) cc_final: 0.8594 (mm) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.3757 time to fit residues: 103.9320 Evaluate side-chains 186 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 2 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 54 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.151942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.097221 restraints weight = 40566.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.102401 restraints weight = 17739.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.105627 restraints weight = 11284.982| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.6100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7374 Z= 0.137 Angle : 0.490 5.000 9987 Z= 0.271 Chirality : 0.042 0.176 1046 Planarity : 0.004 0.065 1309 Dihedral : 4.095 19.880 1003 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.27), residues: 879 helix: 1.01 (0.39), residues: 190 sheet: -0.04 (0.24), residues: 369 loop : -0.12 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 576 HIS 0.002 0.000 HIS A 533 PHE 0.014 0.001 PHE P1278 TYR 0.014 0.001 TYR D 184 ARG 0.006 0.000 ARG D 173 Details of bonding type rmsd hydrogen bonds : bond 0.03183 ( 394) hydrogen bonds : angle 5.04568 ( 1206) SS BOND : bond 0.00566 ( 2) SS BOND : angle 3.39221 ( 4) covalent geometry : bond 0.00292 ( 7372) covalent geometry : angle 0.48509 ( 9983) *********************** 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 : 1.162 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: symmetry clash revert: symmetry clash REVERT: P 1159 TYR cc_start: 0.6491 (t80) cc_final: 0.6031 (t80) REVERT: P 1270 ASP cc_start: 0.8729 (t70) cc_final: 0.8296 (t0) REVERT: P 1271 ASN cc_start: 0.8690 (p0) cc_final: 0.8311 (p0) REVERT: A 284 ILE cc_start: 0.9210 (mm) cc_final: 0.8564 (tp) REVERT: A 307 ASP cc_start: 0.8455 (t70) cc_final: 0.8155 (t0) REVERT: A 557 SER cc_start: 0.9074 (m) cc_final: 0.8696 (t) REVERT: A 582 ASP cc_start: 0.8877 (t70) cc_final: 0.8644 (t0) REVERT: A 630 LEU cc_start: 0.8667 (tp) cc_final: 0.8390 (tp) REVERT: A 666 ASN cc_start: 0.9281 (m-40) cc_final: 0.8986 (m-40) REVERT: A 740 ASP cc_start: 0.6591 (m-30) cc_final: 0.6336 (m-30) REVERT: D 84 ASP cc_start: 0.8040 (m-30) cc_final: 0.7427 (m-30) REVERT: D 127 PHE cc_start: 0.8488 (t80) cc_final: 0.8271 (t80) REVERT: D 132 ARG cc_start: 0.8354 (mmm-85) cc_final: 0.7451 (mtp85) REVERT: D 187 GLU cc_start: 0.9083 (tp30) cc_final: 0.8791 (tp30) REVERT: E 31 ASP cc_start: 0.8473 (m-30) cc_final: 0.8067 (m-30) REVERT: E 65 SER cc_start: 0.9182 (p) cc_final: 0.8863 (t) REVERT: E 104 ILE cc_start: 0.8855 (pt) cc_final: 0.8604 (mm) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.4273 time to fit residues: 115.3127 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 : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 30 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 4 optimal weight: 30.0000 chunk 21 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 226 GLN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.152124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.096121 restraints weight = 41309.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.101208 restraints weight = 18786.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.104372 restraints weight = 12188.059| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.6180 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= 0.150 Angle : 0.508 5.090 9987 Z= 0.279 Chirality : 0.042 0.179 1046 Planarity : 0.004 0.067 1309 Dihedral : 4.120 17.231 1003 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.28), residues: 879 helix: 1.00 (0.39), residues: 190 sheet: -0.09 (0.24), residues: 371 loop : -0.20 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 576 HIS 0.002 0.001 HIS A 533 PHE 0.023 0.001 PHE A 586 TYR 0.014 0.001 TYR A 585 ARG 0.007 0.001 ARG D 173 Details of bonding type rmsd hydrogen bonds : bond 0.03207 ( 394) hydrogen bonds : angle 5.03350 ( 1206) SS BOND : bond 0.00567 ( 2) SS BOND : angle 3.23714 ( 4) covalent geometry : bond 0.00321 ( 7372) covalent geometry : angle 0.50388 ( 9983) ********************** 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 200 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 1.179 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: 0.6526 (t80) cc_final: 0.6128 (t80) REVERT: P 1270 ASP cc_start: 0.8687 (t70) cc_final: 0.8258 (t0) REVERT: P 1271 ASN cc_start: 0.8696 (p0) cc_final: 0.8323 (p0) REVERT: A 284 ILE cc_start: 0.9211 (mm) cc_final: 0.8570 (tp) REVERT: A 307 ASP cc_start: 0.8432 (t70) cc_final: 0.8125 (t0) REVERT: A 557 SER cc_start: 0.9092 (m) cc_final: 0.8702 (t) REVERT: A 582 ASP cc_start: 0.8855 (t70) cc_final: 0.8636 (t0) REVERT: A 630 LEU cc_start: 0.8704 (tp) cc_final: 0.8426 (tp) REVERT: A 648 PHE cc_start: 0.9271 (p90) cc_final: 0.8991 (p90) REVERT: A 666 ASN cc_start: 0.9260 (m-40) cc_final: 0.8973 (m-40) REVERT: A 740 ASP cc_start: 0.6569 (m-30) cc_final: 0.6304 (m-30) REVERT: C 56 MET cc_start: 0.8222 (mtp) cc_final: 0.7915 (mmm) REVERT: D 84 ASP cc_start: 0.8050 (m-30) cc_final: 0.7450 (m-30) REVERT: D 127 PHE cc_start: 0.8456 (t80) cc_final: 0.8253 (t80) REVERT: D 132 ARG cc_start: 0.8428 (mmm-85) cc_final: 0.7521 (mtp85) REVERT: E 31 ASP cc_start: 0.8467 (m-30) cc_final: 0.8059 (m-30) REVERT: E 65 SER cc_start: 0.9098 (p) cc_final: 0.8788 (t) REVERT: E 104 ILE cc_start: 0.8809 (pt) cc_final: 0.8604 (mm) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.4400 time to fit residues: 119.1088 Evaluate side-chains 178 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 241 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.152970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.099013 restraints weight = 41003.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.103994 restraints weight = 18901.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.107044 restraints weight = 12300.461| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.6287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 7374 Z= 0.115 Angle : 0.505 9.329 9987 Z= 0.273 Chirality : 0.042 0.177 1046 Planarity : 0.004 0.063 1309 Dihedral : 4.070 18.539 1003 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.28), residues: 879 helix: 0.99 (0.40), residues: 190 sheet: -0.00 (0.24), residues: 369 loop : -0.25 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 576 HIS 0.003 0.000 HIS A 533 PHE 0.016 0.001 PHE P1278 TYR 0.012 0.001 TYR D 184 ARG 0.007 0.000 ARG D 173 Details of bonding type rmsd hydrogen bonds : bond 0.03073 ( 394) hydrogen bonds : angle 4.92126 ( 1206) SS BOND : bond 0.00517 ( 2) SS BOND : angle 3.09015 ( 4) covalent geometry : bond 0.00261 ( 7372) covalent geometry : angle 0.50083 ( 9983) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5897.56 seconds wall clock time: 103 minutes 6.41 seconds (6186.41 seconds total)