Starting phenix.real_space_refine on Wed Sep 17 06:37:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cal_45395/09_2025/9cal_45395_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cal_45395/09_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_45395/09_2025/9cal_45395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cal_45395/09_2025/9cal_45395.map" model { file = "/net/cci-nas-00/data/ceres_data/9cal_45395/09_2025/9cal_45395_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cal_45395/09_2025/9cal_45395_neut.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.50, per 1000 atoms: 0.24 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: 0.59 Conformation dependent library (CDL) restraints added in 291.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.69 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: 0.92 Time building geometry restraints manager: 0.68 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: 2.820 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.630 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.940 ------------------------------------------------------------------------------- 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 6416 Z= 0.211 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (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 ARG 0.006 0.000 ARG A 107 TYR 0.010 0.001 TYR A 240 PHE 0.009 0.001 PHE A 101 TRP 0.020 0.002 TRP A 115 HIS 0.003 0.001 HIS A 29 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 6415) covalent geometry : angle 0.68014 ( 8722) hydrogen bonds : bond 0.19405 ( 267) hydrogen bonds : angle 5.61181 ( 756) Misc. bond : bond 0.03671 ( 1) *********************** 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 : 0.237 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: 0.0992 time to fit residues: 21.1483 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 : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.0970 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.3980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.0870 overall best weight: 0.3758 ------------------------------------------------------------------------------- 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 156 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.110147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.099035 restraints weight = 9715.725| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.03 r_work: 0.3146 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6416 Z= 0.139 Angle : 0.524 5.759 8722 Z= 0.278 Chirality : 0.041 0.198 977 Planarity : 0.004 0.071 1092 Dihedral : 11.227 89.751 946 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.05 % Allowed : 7.95 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.31), residues: 766 helix: 1.42 (0.30), residues: 305 sheet: -0.44 (0.49), residues: 125 loop : -0.37 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 107 TYR 0.012 0.001 TYR A 578 PHE 0.012 0.001 PHE A 433 TRP 0.006 0.001 TRP A 458 HIS 0.003 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 6415) covalent geometry : angle 0.52381 ( 8722) hydrogen bonds : bond 0.04767 ( 267) hydrogen bonds : angle 4.20273 ( 756) Misc. bond : bond 0.00089 ( 1) *********************** 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 175 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 168 time to evaluate : 0.261 Fit side-chains REVERT: A 19 LYS cc_start: 0.8750 (ttpt) cc_final: 0.8542 (ttpt) REVERT: A 162 ASN cc_start: 0.7776 (m-40) cc_final: 0.7355 (m-40) REVERT: A 423 ASP cc_start: 0.8252 (m-30) cc_final: 0.7951 (m-30) REVERT: A 587 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7854 (m-30) REVERT: A 599 SER cc_start: 0.8313 (t) cc_final: 0.8034 (t) REVERT: B 132 ILE cc_start: 0.8661 (mm) cc_final: 0.8405 (mm) outliers start: 7 outliers final: 3 residues processed: 168 average time/residue: 0.0879 time to fit residues: 18.6976 Evaluate side-chains 165 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 161 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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 70 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 0.1980 chunk 52 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 48 optimal weight: 0.0050 chunk 13 optimal weight: 0.4980 overall best weight: 0.4994 ------------------------------------------------------------------------------- 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 = 0.3416 r_free = 0.3416 target = 0.109751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.098643 restraints weight = 9714.781| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.03 r_work: 0.3139 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6416 Z= 0.156 Angle : 0.518 5.897 8722 Z= 0.274 Chirality : 0.041 0.175 977 Planarity : 0.004 0.060 1092 Dihedral : 11.149 88.527 946 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.65 % Allowed : 10.94 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.31), residues: 766 helix: 1.57 (0.30), residues: 305 sheet: -0.31 (0.46), residues: 142 loop : -0.40 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 107 TYR 0.015 0.001 TYR A 578 PHE 0.009 0.001 PHE A 101 TRP 0.007 0.001 TRP A 458 HIS 0.004 0.001 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 6415) covalent geometry : angle 0.51756 ( 8722) hydrogen bonds : bond 0.04476 ( 267) hydrogen bonds : angle 4.04597 ( 756) Misc. bond : bond 0.00024 ( 1) *********************** 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 174 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 163 time to evaluate : 0.209 Fit side-chains REVERT: A 423 ASP cc_start: 0.8301 (m-30) cc_final: 0.7917 (m-30) REVERT: A 504 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7150 (tm-30) REVERT: A 587 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7826 (m-30) REVERT: A 598 ASP cc_start: 0.8304 (m-30) cc_final: 0.7184 (t0) REVERT: A 599 SER cc_start: 0.8276 (t) cc_final: 0.8007 (t) REVERT: B 132 ILE cc_start: 0.8687 (mm) cc_final: 0.8440 (mm) outliers start: 11 outliers final: 7 residues processed: 164 average time/residue: 0.0890 time to fit residues: 18.3764 Evaluate side-chains 168 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 160 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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 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 50 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 27 optimal weight: 0.0980 chunk 63 optimal weight: 0.0570 chunk 22 optimal weight: 0.0970 chunk 4 optimal weight: 0.1980 chunk 8 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.2296 ------------------------------------------------------------------------------- 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 = 0.3436 r_free = 0.3436 target = 0.111119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.099895 restraints weight = 9680.943| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.05 r_work: 0.3160 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6416 Z= 0.104 Angle : 0.482 5.664 8722 Z= 0.254 Chirality : 0.039 0.170 977 Planarity : 0.004 0.053 1092 Dihedral : 11.032 84.358 946 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.65 % Allowed : 13.49 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.31), residues: 766 helix: 1.68 (0.31), residues: 305 sheet: -0.35 (0.47), residues: 140 loop : -0.34 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 107 TYR 0.012 0.001 TYR A 578 PHE 0.008 0.001 PHE A 195 TRP 0.006 0.001 TRP A 241 HIS 0.003 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 6415) covalent geometry : angle 0.48209 ( 8722) hydrogen bonds : bond 0.03752 ( 267) hydrogen bonds : angle 3.89008 ( 756) Misc. bond : bond 0.00006 ( 1) *********************** 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 174 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 163 time to evaluate : 0.207 Fit side-chains REVERT: A 145 LYS cc_start: 0.8775 (mtpt) cc_final: 0.8514 (mtpp) REVERT: A 504 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7127 (tm-30) REVERT: A 552 ASP cc_start: 0.7971 (t0) cc_final: 0.7743 (t0) REVERT: A 599 SER cc_start: 0.8241 (t) cc_final: 0.7927 (t) outliers start: 11 outliers final: 8 residues processed: 164 average time/residue: 0.0973 time to fit residues: 20.1126 Evaluate side-chains 164 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 156 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 425 LYS 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 33 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 1 optimal weight: 0.3980 chunk 59 optimal weight: 0.3980 chunk 7 optimal weight: 0.0770 chunk 44 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 = 0.3421 r_free = 0.3421 target = 0.110028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.098738 restraints weight = 9836.268| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.05 r_work: 0.3145 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6416 Z= 0.140 Angle : 0.502 5.552 8722 Z= 0.265 Chirality : 0.040 0.169 977 Planarity : 0.004 0.057 1092 Dihedral : 10.968 80.642 946 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.50 % Allowed : 16.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.32), residues: 766 helix: 1.76 (0.31), residues: 303 sheet: -0.20 (0.48), residues: 140 loop : -0.34 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 107 TYR 0.015 0.001 TYR A 578 PHE 0.008 0.001 PHE A 127 TRP 0.006 0.001 TRP A 458 HIS 0.003 0.001 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 6415) covalent geometry : angle 0.50194 ( 8722) hydrogen bonds : bond 0.04060 ( 267) hydrogen bonds : angle 3.87985 ( 756) Misc. bond : bond 0.00021 ( 1) *********************** 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 166 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 156 time to evaluate : 0.168 Fit side-chains REVERT: A 33 ASN cc_start: 0.8098 (m-40) cc_final: 0.7874 (t0) REVERT: A 48 GLN cc_start: 0.8217 (mm110) cc_final: 0.8009 (tp40) REVERT: A 145 LYS cc_start: 0.8766 (mtpt) cc_final: 0.8520 (mtpp) REVERT: A 504 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7147 (tm-30) REVERT: A 599 SER cc_start: 0.8268 (t) cc_final: 0.7957 (t) outliers start: 10 outliers final: 7 residues processed: 156 average time/residue: 0.0930 time to fit residues: 18.2126 Evaluate side-chains 159 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 152 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET 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 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 24 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3396 r_free = 0.3396 target = 0.108266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.097204 restraints weight = 9760.951| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.01 r_work: 0.3118 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6416 Z= 0.223 Angle : 0.545 5.170 8722 Z= 0.287 Chirality : 0.043 0.183 977 Planarity : 0.004 0.054 1092 Dihedral : 10.945 77.057 946 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.40 % Allowed : 16.49 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.31), residues: 766 helix: 1.64 (0.31), residues: 302 sheet: -0.27 (0.49), residues: 127 loop : -0.44 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 107 TYR 0.018 0.002 TYR A 578 PHE 0.011 0.002 PHE A 127 TRP 0.009 0.001 TRP A 115 HIS 0.006 0.001 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00530 ( 6415) covalent geometry : angle 0.54517 ( 8722) hydrogen bonds : bond 0.04650 ( 267) hydrogen bonds : angle 3.95269 ( 756) Misc. bond : bond 0.00039 ( 1) *********************** 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 179 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.227 Fit side-chains REVERT: A 4 VAL cc_start: 0.8712 (OUTLIER) cc_final: 0.8510 (m) REVERT: A 9 GLU cc_start: 0.7316 (tt0) cc_final: 0.7101 (tt0) REVERT: A 15 GLN cc_start: 0.8063 (tm-30) cc_final: 0.7638 (tt0) REVERT: A 145 LYS cc_start: 0.8802 (mtpt) cc_final: 0.8594 (mtpp) REVERT: A 504 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7172 (tm-30) REVERT: A 599 SER cc_start: 0.8326 (t) cc_final: 0.7999 (t) outliers start: 16 outliers final: 12 residues processed: 166 average time/residue: 0.0964 time to fit residues: 20.2592 Evaluate side-chains 172 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL 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 478 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 48 ILE 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 33 optimal weight: 0.9990 chunk 66 optimal weight: 0.3980 chunk 43 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 39 optimal weight: 0.3980 chunk 35 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 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 = 0.3405 r_free = 0.3405 target = 0.108910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.097854 restraints weight = 9734.416| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.02 r_work: 0.3130 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6416 Z= 0.172 Angle : 0.535 6.620 8722 Z= 0.281 Chirality : 0.041 0.169 977 Planarity : 0.004 0.051 1092 Dihedral : 10.941 75.161 946 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.25 % Allowed : 16.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.31), residues: 766 helix: 1.58 (0.31), residues: 304 sheet: -0.14 (0.47), residues: 142 loop : -0.41 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 107 TYR 0.016 0.002 TYR A 578 PHE 0.010 0.001 PHE A 127 TRP 0.008 0.001 TRP A 115 HIS 0.004 0.001 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 6415) covalent geometry : angle 0.53485 ( 8722) hydrogen bonds : bond 0.04367 ( 267) hydrogen bonds : angle 3.96608 ( 756) Misc. bond : bond 0.00027 ( 1) *********************** 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 171 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.209 Fit side-chains REVERT: A 4 VAL cc_start: 0.8692 (OUTLIER) cc_final: 0.8490 (m) REVERT: A 15 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7618 (tt0) REVERT: A 32 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8779 (pp) REVERT: A 48 GLN cc_start: 0.8243 (mm110) cc_final: 0.8031 (tp40) REVERT: A 145 LYS cc_start: 0.8761 (mtpt) cc_final: 0.8552 (mtpp) REVERT: A 504 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7153 (tm-30) REVERT: A 599 SER cc_start: 0.8327 (t) cc_final: 0.7991 (t) outliers start: 15 outliers final: 12 residues processed: 160 average time/residue: 0.0954 time to fit residues: 19.3137 Evaluate side-chains 168 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL 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 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 A residue 439 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 9 LEU 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 30 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 7 optimal weight: 0.0980 chunk 49 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.0970 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.109781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.098643 restraints weight = 9758.635| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.03 r_work: 0.3144 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6416 Z= 0.131 Angle : 0.509 7.631 8722 Z= 0.267 Chirality : 0.040 0.164 977 Planarity : 0.004 0.049 1092 Dihedral : 10.940 71.989 946 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.95 % Allowed : 17.69 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.31), residues: 766 helix: 1.71 (0.31), residues: 304 sheet: -0.11 (0.46), residues: 142 loop : -0.31 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 107 TYR 0.014 0.001 TYR A 578 PHE 0.009 0.001 PHE A 127 TRP 0.007 0.001 TRP A 241 HIS 0.003 0.001 HIS A 29 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 6415) covalent geometry : angle 0.50932 ( 8722) hydrogen bonds : bond 0.03958 ( 267) hydrogen bonds : angle 3.87351 ( 756) Misc. bond : bond 0.00028 ( 1) *********************** 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: 13 poor density : 156 time to evaluate : 0.138 Fit side-chains REVERT: A 15 GLN cc_start: 0.8037 (tm-30) cc_final: 0.7607 (tt0) REVERT: A 32 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8616 (pp) REVERT: A 98 MET cc_start: 0.8028 (mmm) cc_final: 0.7001 (mmm) REVERT: A 145 LYS cc_start: 0.8747 (mtpt) cc_final: 0.8534 (mtpp) REVERT: A 504 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7127 (tm-30) REVERT: A 599 SER cc_start: 0.8296 (t) cc_final: 0.7936 (t) outliers start: 13 outliers final: 8 residues processed: 163 average time/residue: 0.0924 time to fit residues: 18.8384 Evaluate side-chains 163 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 A residue 439 LEU Chi-restraints excluded: chain B residue 9 LEU 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 21 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3397 r_free = 0.3397 target = 0.108351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.097276 restraints weight = 9851.336| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.03 r_work: 0.3121 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6416 Z= 0.207 Angle : 0.554 8.311 8722 Z= 0.290 Chirality : 0.043 0.174 977 Planarity : 0.004 0.049 1092 Dihedral : 11.042 71.904 946 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.65 % Allowed : 17.99 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.31), residues: 766 helix: 1.59 (0.31), residues: 303 sheet: -0.18 (0.46), residues: 140 loop : -0.43 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 107 TYR 0.017 0.002 TYR A 578 PHE 0.012 0.001 PHE A 127 TRP 0.009 0.001 TRP A 115 HIS 0.005 0.001 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00492 ( 6415) covalent geometry : angle 0.55437 ( 8722) hydrogen bonds : bond 0.04518 ( 267) hydrogen bonds : angle 3.96157 ( 756) Misc. bond : bond 0.00060 ( 1) *********************** 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: 11 poor density : 157 time to evaluate : 0.231 Fit side-chains REVERT: A 15 GLN cc_start: 0.8070 (tm-30) cc_final: 0.7617 (tt0) REVERT: A 32 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8649 (pp) REVERT: A 48 GLN cc_start: 0.8271 (mm110) cc_final: 0.8054 (tp40) REVERT: A 98 MET cc_start: 0.8044 (mmm) cc_final: 0.7654 (mmp) REVERT: A 145 LYS cc_start: 0.8761 (mtpt) cc_final: 0.8556 (mtpp) REVERT: A 504 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7157 (tm-30) REVERT: A 599 SER cc_start: 0.8347 (t) cc_final: 0.8006 (t) outliers start: 11 outliers final: 9 residues processed: 161 average time/residue: 0.1008 time to fit residues: 20.3602 Evaluate side-chains 165 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 155 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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 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 51 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 39 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 25 optimal weight: 0.0070 chunk 73 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 42 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 6 optimal weight: 0.1980 overall best weight: 0.4198 ------------------------------------------------------------------------------- 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 = 0.3411 r_free = 0.3411 target = 0.109433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.098344 restraints weight = 9662.854| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.01 r_work: 0.3138 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6416 Z= 0.138 Angle : 0.506 5.029 8722 Z= 0.267 Chirality : 0.040 0.161 977 Planarity : 0.004 0.048 1092 Dihedral : 11.183 70.755 946 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.95 % Allowed : 17.69 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.31), residues: 766 helix: 1.61 (0.31), residues: 304 sheet: -0.23 (0.46), residues: 140 loop : -0.33 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 107 TYR 0.015 0.001 TYR A 578 PHE 0.009 0.001 PHE A 127 TRP 0.007 0.001 TRP A 241 HIS 0.003 0.001 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 6415) covalent geometry : angle 0.50590 ( 8722) hydrogen bonds : bond 0.03990 ( 267) hydrogen bonds : angle 3.88423 ( 756) Misc. bond : bond 0.00032 ( 1) ********************** 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 163 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.152 Fit side-chains REVERT: A 32 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8652 (pp) REVERT: A 98 MET cc_start: 0.8008 (mmm) cc_final: 0.7629 (mmp) REVERT: A 145 LYS cc_start: 0.8743 (mtpt) cc_final: 0.8541 (mtpp) REVERT: A 164 MET cc_start: 0.8780 (tpt) cc_final: 0.8576 (mmm) REVERT: A 504 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7092 (tm-30) REVERT: A 599 SER cc_start: 0.8309 (t) cc_final: 0.7961 (t) REVERT: A 606 LEU cc_start: 0.8143 (mt) cc_final: 0.7889 (mp) outliers start: 13 outliers final: 10 residues processed: 155 average time/residue: 0.1006 time to fit residues: 19.4901 Evaluate side-chains 159 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 286 GLU 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 51 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 75 optimal weight: 0.9980 chunk 63 optimal weight: 0.1980 chunk 32 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 21 optimal weight: 0.3980 chunk 13 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.108841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.097804 restraints weight = 9782.839| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.02 r_work: 0.3134 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6416 Z= 0.160 Angle : 0.522 6.513 8722 Z= 0.275 Chirality : 0.041 0.159 977 Planarity : 0.004 0.048 1092 Dihedral : 11.282 70.296 946 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.65 % Allowed : 18.44 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.31), residues: 766 helix: 1.61 (0.31), residues: 304 sheet: -0.27 (0.46), residues: 140 loop : -0.34 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 107 TYR 0.016 0.001 TYR A 578 PHE 0.010 0.001 PHE A 127 TRP 0.007 0.001 TRP A 115 HIS 0.004 0.001 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 6415) covalent geometry : angle 0.52185 ( 8722) hydrogen bonds : bond 0.04147 ( 267) hydrogen bonds : angle 3.89290 ( 756) Misc. bond : bond 0.00033 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1658.13 seconds wall clock time: 29 minutes 6.58 seconds (1746.58 seconds total)