Starting phenix.real_space_refine on Tue Feb 11 16:21:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cal_45395/02_2025/9cal_45395_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cal_45395/02_2025/9cal_45395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cal_45395/02_2025/9cal_45395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cal_45395/02_2025/9cal_45395.map" model { file = "/net/cci-nas-00/data/ceres_data/9cal_45395/02_2025/9cal_45395_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cal_45395/02_2025/9cal_45395_neut.cif" } resolution = 3.15 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= 0.001 sd= 0.020 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: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 P 10 5.49 5 S 39 5.16 5 C 3928 2.51 5 N 1084 2.21 5 O 1206 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6268 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4845 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 30, 'TRANS': 581} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1219 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "D" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 146 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "E" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Classifications: {'DNA': 3} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.80, per 1000 atoms: 0.77 Number of scatterers: 6268 At special positions: 0 Unit cell: (72.16, 86.1, 137.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 1 24.99 S 39 16.00 P 10 15.00 O 1206 8.00 N 1084 7.00 C 3928 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 907.3 milliseconds 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1442 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 6 sheets defined 42.8% alpha, 14.7% beta 0 base pairs and 5 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 77 through 82 removed outlier: 3.997A pdb=" N PHE A 82 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 106 Processing helix chain 'A' and resid 119 through 134 Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 156 through 166 Processing helix chain 'A' and resid 171 through 201 removed outlier: 3.743A pdb=" N ALA A 191 " --> pdb=" O ARG A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 234 removed outlier: 3.725A pdb=" N CYS A 225 " --> pdb=" O THR A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 277 removed outlier: 3.523A pdb=" N THR A 277 " --> pdb=" O PHE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 313 Processing helix chain 'A' and resid 317 through 332 Processing helix chain 'A' and resid 349 through 357 removed outlier: 4.146A pdb=" N GLN A 357 " --> pdb=" O SER A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 373 Processing helix chain 'A' and resid 404 through 421 removed outlier: 3.730A pdb=" N LEU A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 455 Processing helix chain 'A' and resid 495 through 507 Processing helix chain 'A' and resid 513 through 524 Processing helix chain 'A' and resid 538 through 552 Processing helix chain 'A' and resid 553 through 556 Processing helix chain 'A' and resid 559 through 573 removed outlier: 3.923A pdb=" N LEU A 570 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE A 571 " --> pdb=" O GLN A 567 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 599 Processing helix chain 'A' and resid 600 through 611 removed outlier: 3.742A pdb=" N LEU A 606 " --> pdb=" O GLY A 602 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL A 609 " --> pdb=" O GLU A 605 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER A 610 " --> pdb=" O LEU A 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 17 through 25 removed outlier: 3.505A pdb=" N THR B 25 " --> pdb=" O ILE B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 41 Processing helix chain 'B' and resid 44 through 48 Processing helix chain 'B' and resid 56 through 60 removed outlier: 4.256A pdb=" N GLY B 60 " --> pdb=" O ILE B 57 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 6.557A pdb=" N LYS A 2 " --> pdb=" O ARG A 51 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LYS A 53 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL A 4 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N THR A 3 " --> pdb=" O TYR A 111 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N VAL A 113 " --> pdb=" O THR A 3 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU A 5 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE A 112 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 66 Processing sheet with id=AA3, first strand: chain 'A' and resid 254 through 256 removed outlier: 6.569A pdb=" N VAL A 242 " --> pdb=" O MET A 483 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N MET A 483 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N GLN A 244 " --> pdb=" O VAL A 481 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL A 481 " --> pdb=" O GLN A 244 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LYS A 246 " --> pdb=" O GLY A 479 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 258 through 259 removed outlier: 7.258A pdb=" N LYS A 425 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR A 426 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 430 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA A 287 " --> pdb=" O SER A 432 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG A 434 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N VAL A 285 " --> pdb=" O ARG A 434 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 527 through 529 Processing sheet with id=AA6, first strand: chain 'B' and resid 135 through 136 removed outlier: 9.347A pdb=" N LEU B 140 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR B 107 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N LEU B 142 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL B 109 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LEU B 95 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ARG B 96 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE B 76 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLN B 98 " --> pdb=" O GLN B 74 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N CYS B 69 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LYS B 126 " --> pdb=" O LEU B 150 " (cutoff:3.500A) 267 hydrogen bonds defined for protein. 756 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 5 stacking parallelities Total time for adding SS restraints: 1.74 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1966 1.34 - 1.45: 875 1.45 - 1.57: 3495 1.57 - 1.69: 18 1.69 - 1.81: 61 Bond restraints: 6415 Sorted by residual: bond pdb=" OH PTR A 336 " pdb=" P PTR A 336 " ideal model delta sigma weight residual 1.769 1.608 0.161 2.00e-02 2.50e+03 6.49e+01 bond pdb=" C SER A 335 " pdb=" N PTR A 336 " ideal model delta sigma weight residual 1.329 1.430 -0.101 1.40e-02 5.10e+03 5.18e+01 bond pdb=" O1P PTR A 336 " pdb=" P PTR A 336 " ideal model delta sigma weight residual 1.522 1.477 0.045 2.00e-02 2.50e+03 5.03e+00 bond pdb=" CZ PTR A 336 " pdb=" OH PTR A 336 " ideal model delta sigma weight residual 1.339 1.300 0.039 2.00e-02 2.50e+03 3.84e+00 bond pdb=" O3' DA D 3 " pdb=" P DT D 4 " ideal model delta sigma weight residual 1.607 1.583 0.024 1.50e-02 4.44e+03 2.58e+00 ... (remaining 6410 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.17: 8716 6.17 - 12.34: 4 12.34 - 18.51: 1 18.51 - 24.68: 0 24.68 - 30.85: 1 Bond angle restraints: 8722 Sorted by residual: angle pdb=" O SER A 335 " pdb=" C SER A 335 " pdb=" N PTR A 336 " ideal model delta sigma weight residual 123.00 92.15 30.85 1.60e+00 3.91e-01 3.72e+02 angle pdb=" CA SER A 335 " pdb=" C SER A 335 " pdb=" N PTR A 336 " ideal model delta sigma weight residual 116.20 132.42 -16.22 2.00e+00 2.50e-01 6.58e+01 angle pdb=" N ASN A 33 " pdb=" CA ASN A 33 " pdb=" C ASN A 33 " ideal model delta sigma weight residual 114.62 109.58 5.04 1.14e+00 7.69e-01 1.95e+01 angle pdb=" C SER A 335 " pdb=" N PTR A 336 " pdb=" CA PTR A 336 " ideal model delta sigma weight residual 121.70 129.53 -7.83 1.80e+00 3.09e-01 1.89e+01 angle pdb=" OH PTR A 336 " pdb=" P PTR A 336 " pdb=" O2P PTR A 336 " ideal model delta sigma weight residual 99.92 109.91 -9.99 3.00e+00 1.11e-01 1.11e+01 ... (remaining 8717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 3434 17.94 - 35.88: 344 35.88 - 53.81: 78 53.81 - 71.75: 9 71.75 - 89.69: 9 Dihedral angle restraints: 3874 sinusoidal: 1640 harmonic: 2234 Sorted by residual: dihedral pdb=" CA LEU A 67 " pdb=" C LEU A 67 " pdb=" N GLY A 68 " pdb=" CA GLY A 68 " ideal model delta harmonic sigma weight residual 180.00 162.78 17.22 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CG ARG A 407 " pdb=" CD ARG A 407 " pdb=" NE ARG A 407 " pdb=" CZ ARG A 407 " ideal model delta sinusoidal sigma weight residual -180.00 -135.06 -44.94 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CB GLU A 238 " pdb=" CG GLU A 238 " pdb=" CD GLU A 238 " pdb=" OE1 GLU A 238 " ideal model delta sinusoidal sigma weight residual 0.00 89.69 -89.69 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 3871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 630 0.032 - 0.064: 248 0.064 - 0.096: 61 0.096 - 0.128: 33 0.128 - 0.160: 5 Chirality restraints: 977 Sorted by residual: chirality pdb=" CA PTR A 336 " pdb=" N PTR A 336 " pdb=" C PTR A 336 " pdb=" CB PTR A 336 " both_signs ideal model delta sigma weight residual False 2.35 2.51 -0.16 2.00e-01 2.50e+01 6.44e-01 chirality pdb=" CA VAL B 31 " pdb=" N VAL B 31 " pdb=" C VAL B 31 " pdb=" CB VAL B 31 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CB VAL A 136 " pdb=" CA VAL A 136 " pdb=" CG1 VAL A 136 " pdb=" CG2 VAL A 136 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 974 not shown) Planarity restraints: 1092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 335 " 0.084 2.00e-02 2.50e+03 1.31e-01 1.73e+02 pdb=" C SER A 335 " -0.227 2.00e-02 2.50e+03 pdb=" O SER A 335 " 0.070 2.00e-02 2.50e+03 pdb=" N PTR A 336 " 0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 476 " -0.067 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO A 477 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO A 477 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 477 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 436 " -0.028 5.00e-02 4.00e+02 4.38e-02 3.06e+00 pdb=" N PRO A 437 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 437 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 437 " -0.024 5.00e-02 4.00e+02 ... (remaining 1089 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 118 2.69 - 3.24: 5871 3.24 - 3.79: 9334 3.79 - 4.35: 12400 4.35 - 4.90: 20681 Nonbonded interactions: 48404 Sorted by model distance: nonbonded pdb=" OD2 ASP A 117 " pdb="MN MN A 701 " model vdw 2.136 2.320 nonbonded pdb=" OD2 ASP A 119 " pdb="MN MN A 701 " model vdw 2.173 2.320 nonbonded pdb=" OE1 GLN A 196 " pdb=" OH TYR A 548 " model vdw 2.241 3.040 nonbonded pdb=" OH TYR A 199 " pdb=" OD2 ASP A 604 " model vdw 2.280 3.040 nonbonded pdb=" OD1 ASP A 208 " pdb=" N SER A 209 " model vdw 2.291 3.120 ... (remaining 48399 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.840 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 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 : 0.004 0.161 6415 Z= 0.266 Angle : 0.680 30.854 8722 Z= 0.369 Chirality : 0.040 0.160 977 Planarity : 0.006 0.131 1092 Dihedral : 15.357 89.687 2432 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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: -0.07 (0.31), residues: 766 helix: 0.71 (0.30), residues: 309 sheet: -0.49 (0.49), residues: 127 loop : -0.46 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 115 HIS 0.003 0.001 HIS A 29 PHE 0.009 0.001 PHE A 101 TYR 0.010 0.001 TYR A 240 ARG 0.006 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: A 48 GLN cc_start: 0.8056 (mm110) cc_final: 0.7737 (tp40) REVERT: A 246 LYS cc_start: 0.8427 (mttm) cc_final: 0.8206 (mttp) REVERT: A 284 GLN cc_start: 0.7664 (mm-40) cc_final: 0.7280 (mm-40) REVERT: A 425 LYS cc_start: 0.8154 (mttm) cc_final: 0.7927 (mttm) REVERT: A 434 ARG cc_start: 0.7894 (ttm170) cc_final: 0.7691 (ttm-80) REVERT: A 599 SER cc_start: 0.7741 (t) cc_final: 0.7518 (t) REVERT: B 132 ILE cc_start: 0.8605 (mm) cc_final: 0.8375 (mm) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.2446 time to fit residues: 52.6780 Evaluate side-chains 161 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 39 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 0.0670 chunk 44 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 218 GLN B 11 GLN B 156 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.109151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.098067 restraints weight = 9697.605| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.04 r_work: 0.3130 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6415 Z= 0.268 Angle : 0.541 6.562 8722 Z= 0.287 Chirality : 0.042 0.200 977 Planarity : 0.004 0.071 1092 Dihedral : 11.256 88.966 946 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.35 % Allowed : 7.95 % Favored : 90.70 % 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: 0.37 (0.31), residues: 766 helix: 1.36 (0.30), residues: 306 sheet: -0.45 (0.49), residues: 125 loop : -0.44 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 458 HIS 0.004 0.001 HIS A 172 PHE 0.011 0.001 PHE A 433 TYR 0.013 0.002 TYR A 578 ARG 0.004 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 163 time to evaluate : 0.741 Fit side-chains REVERT: A 423 ASP cc_start: 0.8257 (m-30) cc_final: 0.7952 (m-30) REVERT: A 587 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7861 (m-30) REVERT: A 599 SER cc_start: 0.8317 (t) cc_final: 0.8044 (t) REVERT: B 132 ILE cc_start: 0.8674 (mm) cc_final: 0.8430 (mm) outliers start: 9 outliers final: 3 residues processed: 163 average time/residue: 0.2219 time to fit residues: 45.6019 Evaluate side-chains 162 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 158 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 21 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 58 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 37 optimal weight: 0.0870 chunk 47 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 46 optimal weight: 0.0000 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN A 573 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.110058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.098991 restraints weight = 9725.949| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.04 r_work: 0.3142 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6415 Z= 0.211 Angle : 0.509 5.906 8722 Z= 0.270 Chirality : 0.041 0.184 977 Planarity : 0.004 0.058 1092 Dihedral : 11.162 88.483 946 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.65 % Allowed : 11.09 % Favored : 87.26 % 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: 0.53 (0.31), residues: 766 helix: 1.58 (0.30), residues: 304 sheet: -0.33 (0.46), residues: 142 loop : -0.44 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 458 HIS 0.004 0.001 HIS A 172 PHE 0.009 0.001 PHE A 433 TYR 0.014 0.001 TYR A 578 ARG 0.003 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 162 time to evaluate : 0.648 Fit side-chains REVERT: A 48 GLN cc_start: 0.8224 (mm110) cc_final: 0.8002 (tp40) REVERT: A 423 ASP cc_start: 0.8286 (m-30) cc_final: 0.7901 (m-30) REVERT: A 504 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7129 (tm-30) REVERT: A 587 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7828 (m-30) REVERT: A 598 ASP cc_start: 0.8300 (m-30) cc_final: 0.7182 (t0) REVERT: A 599 SER cc_start: 0.8268 (t) cc_final: 0.7997 (t) REVERT: B 132 ILE cc_start: 0.8677 (mm) cc_final: 0.8426 (mm) outliers start: 11 outliers final: 8 residues processed: 164 average time/residue: 0.2193 time to fit residues: 45.1221 Evaluate side-chains 168 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 159 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 51 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 14 optimal weight: 0.1980 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.109365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.098195 restraints weight = 9760.751| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.04 r_work: 0.3130 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6415 Z= 0.256 Angle : 0.517 5.650 8722 Z= 0.273 Chirality : 0.041 0.169 977 Planarity : 0.004 0.054 1092 Dihedral : 11.052 83.525 946 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.10 % Allowed : 13.64 % Favored : 84.26 % 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: 0.55 (0.31), residues: 766 helix: 1.60 (0.31), residues: 305 sheet: -0.34 (0.47), residues: 140 loop : -0.43 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 458 HIS 0.005 0.001 HIS A 172 PHE 0.010 0.001 PHE A 101 TYR 0.016 0.001 TYR A 578 ARG 0.004 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 0.731 Fit side-chains REVERT: A 383 ASP cc_start: 0.7724 (t0) cc_final: 0.7507 (t0) REVERT: A 423 ASP cc_start: 0.8302 (m-30) cc_final: 0.7931 (m-30) REVERT: A 504 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7161 (tm-30) REVERT: A 587 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7798 (m-30) REVERT: A 598 ASP cc_start: 0.8276 (m-30) cc_final: 0.7219 (t0) REVERT: A 599 SER cc_start: 0.8283 (t) cc_final: 0.8010 (t) REVERT: B 132 ILE cc_start: 0.8695 (mm) cc_final: 0.8454 (mm) outliers start: 14 outliers final: 10 residues processed: 164 average time/residue: 0.2214 time to fit residues: 46.4292 Evaluate side-chains 175 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 164 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 51 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 11 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 61 optimal weight: 0.0870 chunk 28 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.3406 r_free = 0.3406 target = 0.108922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.097769 restraints weight = 9732.927| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.04 r_work: 0.3126 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6415 Z= 0.275 Angle : 0.521 5.374 8722 Z= 0.276 Chirality : 0.042 0.174 977 Planarity : 0.004 0.051 1092 Dihedral : 10.999 79.005 946 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.95 % Allowed : 14.84 % Favored : 83.21 % 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 (0.31), residues: 766 helix: 1.65 (0.31), residues: 301 sheet: -0.24 (0.47), residues: 140 loop : -0.45 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 115 HIS 0.005 0.001 HIS A 172 PHE 0.010 0.001 PHE A 127 TYR 0.017 0.002 TYR A 578 ARG 0.004 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 0.718 Fit side-chains REVERT: A 48 GLN cc_start: 0.8254 (mm110) cc_final: 0.8022 (tp40) REVERT: A 383 ASP cc_start: 0.7744 (t0) cc_final: 0.7506 (t0) REVERT: A 423 ASP cc_start: 0.8315 (m-30) cc_final: 0.7911 (m-30) REVERT: A 504 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7173 (tm-30) REVERT: A 587 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7809 (m-30) REVERT: A 598 ASP cc_start: 0.8285 (m-30) cc_final: 0.7636 (m-30) REVERT: A 599 SER cc_start: 0.8327 (t) cc_final: 0.8029 (t) REVERT: B 132 ILE cc_start: 0.8712 (mm) cc_final: 0.8481 (mm) outliers start: 13 outliers final: 9 residues processed: 166 average time/residue: 0.2385 time to fit residues: 49.6275 Evaluate side-chains 172 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 162 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 51 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 28 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 40 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.108463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.097504 restraints weight = 9646.625| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.01 r_work: 0.3123 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6415 Z= 0.307 Angle : 0.533 5.803 8722 Z= 0.282 Chirality : 0.042 0.169 977 Planarity : 0.004 0.049 1092 Dihedral : 10.967 75.687 946 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.95 % Allowed : 16.19 % Favored : 81.86 % 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: 0.56 (0.31), residues: 766 helix: 1.63 (0.31), residues: 301 sheet: -0.26 (0.47), residues: 140 loop : -0.46 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 73 HIS 0.005 0.001 HIS A 172 PHE 0.011 0.001 PHE A 127 TYR 0.017 0.002 TYR A 578 ARG 0.003 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 0.691 Fit side-chains REVERT: A 33 ASN cc_start: 0.8030 (m-40) cc_final: 0.7737 (t0) REVERT: A 48 GLN cc_start: 0.8260 (mm110) cc_final: 0.8033 (tp40) REVERT: A 74 ASP cc_start: 0.8103 (t0) cc_final: 0.7877 (m-30) REVERT: A 162 ASN cc_start: 0.7788 (m-40) cc_final: 0.7362 (m-40) REVERT: A 504 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7172 (tm-30) REVERT: A 599 SER cc_start: 0.8336 (t) cc_final: 0.7984 (t) REVERT: B 132 ILE cc_start: 0.8715 (mm) cc_final: 0.8479 (mm) outliers start: 13 outliers final: 11 residues processed: 165 average time/residue: 0.2125 time to fit residues: 44.1384 Evaluate side-chains 166 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 155 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 51 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 66 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.108039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.097105 restraints weight = 9727.855| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.02 r_work: 0.3115 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 6415 Z= 0.309 Angle : 0.539 6.030 8722 Z= 0.285 Chirality : 0.042 0.168 977 Planarity : 0.004 0.048 1092 Dihedral : 11.024 73.827 946 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.40 % Allowed : 15.89 % Favored : 81.71 % 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: 0.51 (0.31), residues: 766 helix: 1.57 (0.31), residues: 302 sheet: -0.28 (0.47), residues: 135 loop : -0.48 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 115 HIS 0.005 0.001 HIS A 172 PHE 0.011 0.001 PHE A 127 TYR 0.018 0.002 TYR A 578 ARG 0.005 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.685 Fit side-chains REVERT: A 32 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8655 (pp) REVERT: A 33 ASN cc_start: 0.7963 (m-40) cc_final: 0.7627 (t0) REVERT: A 48 GLN cc_start: 0.8262 (mm110) cc_final: 0.8030 (tp40) REVERT: A 74 ASP cc_start: 0.8084 (t0) cc_final: 0.7877 (m-30) REVERT: A 162 ASN cc_start: 0.7773 (m-40) cc_final: 0.7341 (m-40) REVERT: A 504 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7165 (tm-30) REVERT: A 599 SER cc_start: 0.8349 (t) cc_final: 0.8004 (t) outliers start: 16 outliers final: 12 residues processed: 162 average time/residue: 0.2407 time to fit residues: 49.1134 Evaluate side-chains 169 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 51 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 59 optimal weight: 0.4980 chunk 2 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 13 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3398 r_free = 0.3398 target = 0.108350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.097326 restraints weight = 9670.128| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.01 r_work: 0.3126 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6415 Z= 0.264 Angle : 0.528 7.555 8722 Z= 0.278 Chirality : 0.041 0.166 977 Planarity : 0.004 0.047 1092 Dihedral : 11.141 72.652 946 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.10 % Allowed : 16.64 % Favored : 81.26 % 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: 0.58 (0.31), residues: 766 helix: 1.59 (0.31), residues: 303 sheet: -0.28 (0.47), residues: 135 loop : -0.40 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 241 HIS 0.004 0.001 HIS A 172 PHE 0.011 0.001 PHE A 127 TYR 0.016 0.002 TYR A 578 ARG 0.005 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 0.741 Fit side-chains REVERT: A 32 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8648 (pp) REVERT: A 33 ASN cc_start: 0.7944 (m-40) cc_final: 0.7636 (t0) REVERT: A 48 GLN cc_start: 0.8253 (mm110) cc_final: 0.8032 (tp40) REVERT: A 74 ASP cc_start: 0.8100 (t0) cc_final: 0.7888 (m-30) REVERT: A 504 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7154 (tm-30) REVERT: A 599 SER cc_start: 0.8320 (t) cc_final: 0.7974 (t) outliers start: 14 outliers final: 12 residues processed: 159 average time/residue: 0.2486 time to fit residues: 49.3926 Evaluate side-chains 164 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 51 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 48 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 0.0030 chunk 61 optimal weight: 0.5980 chunk 32 optimal weight: 0.2980 chunk 66 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- 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 = 0.3405 r_free = 0.3405 target = 0.108985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.097962 restraints weight = 9670.678| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.01 r_work: 0.3136 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6415 Z= 0.219 Angle : 0.533 8.550 8722 Z= 0.276 Chirality : 0.041 0.164 977 Planarity : 0.004 0.047 1092 Dihedral : 11.285 71.675 946 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.95 % Allowed : 17.24 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.31), residues: 766 helix: 1.59 (0.31), residues: 304 sheet: -0.23 (0.47), residues: 133 loop : -0.31 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 241 HIS 0.003 0.001 HIS A 29 PHE 0.010 0.001 PHE A 433 TYR 0.016 0.001 TYR A 578 ARG 0.005 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 0.680 Fit side-chains REVERT: A 32 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8629 (pp) REVERT: A 33 ASN cc_start: 0.7947 (m-40) cc_final: 0.7651 (t0) REVERT: A 145 LYS cc_start: 0.8770 (mtpt) cc_final: 0.8547 (mtpp) REVERT: A 504 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7135 (tm-30) REVERT: A 599 SER cc_start: 0.8290 (t) cc_final: 0.7941 (t) outliers start: 13 outliers final: 9 residues processed: 161 average time/residue: 0.2309 time to fit residues: 46.7987 Evaluate side-chains 157 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 51 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 45 optimal weight: 0.0980 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 14 optimal weight: 0.0970 chunk 47 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 13 optimal weight: 0.1980 chunk 76 optimal weight: 0.7980 overall best weight: 0.2978 ------------------------------------------------------------------------------- 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 = 0.3417 r_free = 0.3417 target = 0.109817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.098675 restraints weight = 9803.583| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.03 r_work: 0.3146 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6415 Z= 0.178 Angle : 0.524 8.448 8722 Z= 0.269 Chirality : 0.040 0.158 977 Planarity : 0.004 0.045 1092 Dihedral : 11.291 70.442 946 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.35 % Allowed : 17.99 % Favored : 80.66 % 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: 0.75 (0.31), residues: 766 helix: 1.73 (0.31), residues: 300 sheet: -0.19 (0.46), residues: 140 loop : -0.27 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 241 HIS 0.003 0.001 HIS A 229 PHE 0.008 0.001 PHE A 127 TYR 0.014 0.001 TYR A 578 ARG 0.006 0.000 ARG A 107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 152 time to evaluate : 0.809 Fit side-chains REVERT: A 15 GLN cc_start: 0.8056 (tm-30) cc_final: 0.7661 (tp40) REVERT: A 32 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8631 (pp) REVERT: A 33 ASN cc_start: 0.7957 (m-40) cc_final: 0.7642 (t0) REVERT: A 145 LYS cc_start: 0.8770 (mtpt) cc_final: 0.8523 (mtpp) REVERT: A 504 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7091 (tm-30) REVERT: A 599 SER cc_start: 0.8285 (t) cc_final: 0.7930 (t) outliers start: 9 outliers final: 8 residues processed: 156 average time/residue: 0.2331 time to fit residues: 45.7257 Evaluate side-chains 159 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 51 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 75 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 65 optimal weight: 0.0470 chunk 67 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 76 optimal weight: 0.0040 chunk 61 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 overall best weight: 0.4290 ------------------------------------------------------------------------------- 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 = 0.3412 r_free = 0.3412 target = 0.109475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.098348 restraints weight = 9802.395| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.03 r_work: 0.3142 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6415 Z= 0.216 Angle : 0.533 8.663 8722 Z= 0.273 Chirality : 0.040 0.154 977 Planarity : 0.004 0.044 1092 Dihedral : 11.279 69.806 946 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.65 % Allowed : 17.69 % Favored : 80.66 % 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 (0.31), residues: 766 helix: 1.64 (0.30), residues: 304 sheet: -0.17 (0.47), residues: 140 loop : -0.31 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 458 HIS 0.003 0.001 HIS A 172 PHE 0.009 0.001 PHE A 127 TYR 0.015 0.001 TYR A 578 ARG 0.006 0.000 ARG A 107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3553.13 seconds wall clock time: 63 minutes 48.57 seconds (3828.57 seconds total)