Starting phenix.real_space_refine on Wed Mar 5 21:46:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tlz_25991/03_2025/7tlz_25991.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tlz_25991/03_2025/7tlz_25991.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tlz_25991/03_2025/7tlz_25991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tlz_25991/03_2025/7tlz_25991.map" model { file = "/net/cci-nas-00/data/ceres_data/7tlz_25991/03_2025/7tlz_25991.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tlz_25991/03_2025/7tlz_25991.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.049 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: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 2359 2.51 5 N 603 2.21 5 O 645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3621 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 761 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 96} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 903 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "J" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1873 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 15, 'TRANS': 235} Chain breaks: 5 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 10, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 90 Chain: "J" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 5.74, per 1000 atoms: 1.59 Number of scatterers: 3621 At special positions: 0 Unit cell: (84.3, 69.126, 76.713, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 645 8.00 N 603 7.00 C 2359 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " distance=2.20 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 15 " - pdb=" SG CYS J 136 " distance=2.04 Simple disulfide: pdb=" SG CYS J 131 " - pdb=" SG CYS J 166 " distance=2.03 Simple disulfide: pdb=" SG CYS J 291 " - pdb=" SG CYS J 301 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG J1401 " - " ASN J 165 " " NAG J1402 " - " ASN J 282 " " NAG J1403 " - " ASN J 17 " " NAG J1404 " - " ASN J 234 " " NAG J1405 " - " ASN J 61 " " NAG J1406 " - " ASN J 122 " Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 408.1 milliseconds 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 884 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 11 sheets defined 4.2% alpha, 50.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'J' and resid 294 through 303 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 4.086A pdb=" N ASP A 70 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A 67 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 6.651A pdb=" N TRP A 35 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N SER A 49 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU A 33 " --> pdb=" O SER A 49 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A 97 " --> pdb=" O GLN A 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54 removed outlier: 6.651A pdb=" N TRP A 35 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N SER A 49 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU A 33 " --> pdb=" O SER A 49 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.702A pdb=" N MET B 34 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N PHE B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12 Processing sheet with id=AA7, first strand: chain 'J' and resid 27 through 30 Processing sheet with id=AA8, first strand: chain 'J' and resid 27 through 30 removed outlier: 8.184A pdb=" N ASN J 61 " --> pdb=" O TYR J 269 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N TYR J 269 " --> pdb=" O ASN J 61 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N PHE J 201 " --> pdb=" O ASP J 228 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASP J 228 " --> pdb=" O PHE J 201 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE J 203 " --> pdb=" O LEU J 226 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 47 through 55 removed outlier: 4.067A pdb=" N ASP J 287 " --> pdb=" O LYS J 278 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 84 through 85 removed outlier: 13.167A pdb=" N PHE J 238 " --> pdb=" O PHE J 133 " (cutoff:3.500A) removed outlier: 13.074A pdb=" N PHE J 135 " --> pdb=" O PHE J 238 " (cutoff:3.500A) removed outlier: 13.017A pdb=" N THR J 240 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 11.290A pdb=" N ASN J 137 " --> pdb=" O THR J 240 " (cutoff:3.500A) removed outlier: 11.225A pdb=" N LEU J 242 " --> pdb=" O ASN J 137 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N LEU J 244 " --> pdb=" O PRO J 139 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU J 141 " --> pdb=" O LEU J 244 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER J 162 " --> pdb=" O GLN J 134 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N CYS J 136 " --> pdb=" O TYR J 160 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TYR J 160 " --> pdb=" O CYS J 136 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASP J 138 " --> pdb=" O ARG J 158 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ARG J 158 " --> pdb=" O ASP J 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 84 through 85 removed outlier: 3.576A pdb=" N GLY J 103 " --> pdb=" O LEU J 241 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA J 243 " --> pdb=" O ILE J 101 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ILE J 101 " --> pdb=" O ALA J 243 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ARG J 102 " --> pdb=" O ASN J 121 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE J 168 " --> pdb=" O VAL J 130 " (cutoff:3.500A) 178 hydrogen bonds defined for protein. 423 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.08 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 636 1.32 - 1.45: 1067 1.45 - 1.58: 1993 1.58 - 1.71: 1 1.71 - 1.84: 18 Bond restraints: 3715 Sorted by residual: bond pdb=" CA ASN J 165 " pdb=" C ASN J 165 " ideal model delta sigma weight residual 1.523 1.582 -0.059 1.42e-02 4.96e+03 1.73e+01 bond pdb=" CA CYS J 131 " pdb=" C CYS J 131 " ideal model delta sigma weight residual 1.522 1.567 -0.046 1.24e-02 6.50e+03 1.36e+01 bond pdb=" C ASN J 165 " pdb=" O ASN J 165 " ideal model delta sigma weight residual 1.235 1.195 0.040 1.20e-02 6.94e+03 1.10e+01 bond pdb=" C5 NAG J1406 " pdb=" O5 NAG J1406 " ideal model delta sigma weight residual 1.413 1.473 -0.060 2.00e-02 2.50e+03 9.10e+00 bond pdb=" C5 NAG J1401 " pdb=" O5 NAG J1401 " ideal model delta sigma weight residual 1.413 1.473 -0.060 2.00e-02 2.50e+03 8.89e+00 ... (remaining 3710 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 4328 1.66 - 3.31: 596 3.31 - 4.97: 88 4.97 - 6.63: 36 6.63 - 8.28: 14 Bond angle restraints: 5062 Sorted by residual: angle pdb=" C LEU J 24 " pdb=" N PRO J 25 " pdb=" CA PRO J 25 " ideal model delta sigma weight residual 119.66 125.78 -6.12 7.20e-01 1.93e+00 7.23e+01 angle pdb=" C ASP J 138 " pdb=" N PRO J 139 " pdb=" CA PRO J 139 " ideal model delta sigma weight residual 119.76 127.46 -7.70 1.00e+00 1.00e+00 5.93e+01 angle pdb=" C PRO J 25 " pdb=" N PRO J 26 " pdb=" CA PRO J 26 " ideal model delta sigma weight residual 119.85 127.21 -7.36 1.01e+00 9.80e-01 5.32e+01 angle pdb=" C GLY A 99 " pdb=" N PRO A 100 " pdb=" CA PRO A 100 " ideal model delta sigma weight residual 119.32 127.60 -8.28 1.14e+00 7.69e-01 5.28e+01 angle pdb=" C ASP J 294 " pdb=" N PRO J 295 " pdb=" CA PRO J 295 " ideal model delta sigma weight residual 119.56 126.43 -6.87 1.02e+00 9.61e-01 4.54e+01 ... (remaining 5057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.38: 2120 14.38 - 28.75: 80 28.75 - 43.13: 17 43.13 - 57.51: 6 57.51 - 71.88: 4 Dihedral angle restraints: 2227 sinusoidal: 849 harmonic: 1378 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 50.62 42.38 1 1.00e+01 1.00e-02 2.51e+01 dihedral pdb=" CA TYR B 95 " pdb=" C TYR B 95 " pdb=" N CYS B 96 " pdb=" CA CYS B 96 " ideal model delta harmonic sigma weight residual 180.00 164.28 15.72 0 5.00e+00 4.00e-02 9.88e+00 dihedral pdb=" CG ARG B 67 " pdb=" CD ARG B 67 " pdb=" NE ARG B 67 " pdb=" CZ ARG B 67 " ideal model delta sinusoidal sigma weight residual 180.00 139.40 40.60 2 1.50e+01 4.44e-03 9.03e+00 ... (remaining 2224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 409 0.071 - 0.142: 128 0.142 - 0.212: 24 0.212 - 0.283: 9 0.283 - 0.354: 5 Chirality restraints: 575 Sorted by residual: chirality pdb=" C2 NAG J1405 " pdb=" C1 NAG J1405 " pdb=" C3 NAG J1405 " pdb=" N2 NAG J1405 " both_signs ideal model delta sigma weight residual False -2.49 -2.85 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" C2 NAG J1401 " pdb=" C1 NAG J1401 " pdb=" C3 NAG J1401 " pdb=" N2 NAG J1401 " both_signs ideal model delta sigma weight residual False -2.49 -2.81 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" C2 NAG J1403 " pdb=" C1 NAG J1403 " pdb=" C3 NAG J1403 " pdb=" N2 NAG J1403 " both_signs ideal model delta sigma weight residual False -2.49 -2.81 0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 572 not shown) Planarity restraints: 650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN J 282 " 0.026 2.00e-02 2.50e+03 2.85e-02 1.01e+01 pdb=" CG ASN J 282 " -0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN J 282 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN J 282 " -0.045 2.00e-02 2.50e+03 pdb=" C1 NAG J1402 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 269 " 0.033 2.00e-02 2.50e+03 1.66e-02 5.54e+00 pdb=" CG TYR J 269 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR J 269 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR J 269 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR J 269 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR J 269 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR J 269 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR J 269 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN J 17 " 0.019 2.00e-02 2.50e+03 1.99e-02 4.94e+00 pdb=" CG ASN J 17 " -0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN J 17 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN J 17 " -0.031 2.00e-02 2.50e+03 pdb=" C1 NAG J1403 " 0.024 2.00e-02 2.50e+03 ... (remaining 647 not shown) Histogram of nonbonded interaction distances: 2.58 - 3.04: 2061 3.04 - 3.51: 3034 3.51 - 3.97: 5566 3.97 - 4.44: 6349 4.44 - 4.90: 10682 Nonbonded interactions: 27692 Sorted by model distance: nonbonded pdb=" O ASP A 92 " pdb=" NH1 ARG B 103 " model vdw 2.581 3.120 nonbonded pdb=" C ASP B 101 " pdb=" OD1 ASP B 101 " model vdw 2.611 3.270 nonbonded pdb=" N ASN J 165 " pdb=" OD1 ASN J 165 " model vdw 2.617 3.120 nonbonded pdb=" N LYS B 76 " pdb=" N ASN B 77 " model vdw 2.628 2.560 nonbonded pdb=" N GLY B 33 " pdb=" O GLY B 33 " model vdw 2.641 2.496 ... (remaining 27687 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: 6.200 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 16.280 Find NCS groups from input model: 0.030 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 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 : 0.011 0.060 3715 Z= 0.704 Angle : 1.301 8.282 5062 Z= 0.878 Chirality : 0.078 0.354 575 Planarity : 0.005 0.021 644 Dihedral : 9.091 71.882 1328 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.31 % Allowed : 0.31 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.02 (0.38), residues: 457 helix: -0.12 (1.59), residues: 11 sheet: 1.60 (0.36), residues: 187 loop : 0.04 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.005 TRP J 64 HIS 0.002 0.001 HIS B 35 PHE 0.016 0.003 PHE A 98 TYR 0.033 0.005 TYR J 269 ARG 0.004 0.001 ARG J 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 202 LYS cc_start: 0.8602 (mttm) cc_final: 0.8380 (mttp) outliers start: 1 outliers final: 1 residues processed: 84 average time/residue: 0.2436 time to fit residues: 23.6649 Evaluate side-chains 60 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 165 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 0.0070 chunk 35 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 0.0060 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 27 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.2814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN B 74 ASN J 66 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.154282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.124222 restraints weight = 4447.175| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.54 r_work: 0.3232 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 3715 Z= 0.179 Angle : 0.569 8.821 5062 Z= 0.304 Chirality : 0.046 0.204 575 Planarity : 0.004 0.026 644 Dihedral : 4.797 25.467 639 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.31 % Allowed : 6.56 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.91 (0.38), residues: 457 helix: 1.76 (1.53), residues: 11 sheet: 1.51 (0.39), residues: 171 loop : -0.01 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 47 HIS 0.002 0.001 HIS J 66 PHE 0.014 0.001 PHE J 79 TYR 0.020 0.001 TYR J 265 ARG 0.004 0.001 ARG B 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.401 Fit side-chains REVERT: J 41 LYS cc_start: 0.7706 (mttt) cc_final: 0.7058 (mtpt) outliers start: 1 outliers final: 1 residues processed: 53 average time/residue: 0.2169 time to fit residues: 13.6729 Evaluate side-chains 51 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 0.2980 chunk 41 optimal weight: 0.0070 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 11 optimal weight: 0.1980 chunk 34 optimal weight: 3.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.149376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.118702 restraints weight = 4498.369| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.81 r_work: 0.3132 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3715 Z= 0.198 Angle : 0.547 6.027 5062 Z= 0.288 Chirality : 0.047 0.210 575 Planarity : 0.004 0.029 644 Dihedral : 4.021 22.215 637 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.31 % Allowed : 7.81 % Favored : 91.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.89 (0.39), residues: 457 helix: 2.48 (1.58), residues: 11 sheet: 1.44 (0.39), residues: 178 loop : -0.06 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 47 HIS 0.004 0.001 HIS J 66 PHE 0.014 0.002 PHE A 98 TYR 0.019 0.001 TYR J 265 ARG 0.002 0.000 ARG J 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.397 Fit side-chains REVERT: J 41 LYS cc_start: 0.7816 (mttt) cc_final: 0.7192 (mtpt) REVERT: J 205 SER cc_start: 0.9195 (p) cc_final: 0.8919 (t) outliers start: 1 outliers final: 0 residues processed: 55 average time/residue: 0.2408 time to fit residues: 15.5900 Evaluate side-chains 49 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 39 optimal weight: 0.0670 chunk 14 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.146270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.115697 restraints weight = 4576.563| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.58 r_work: 0.3123 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3715 Z= 0.245 Angle : 0.563 6.474 5062 Z= 0.293 Chirality : 0.047 0.203 575 Planarity : 0.004 0.037 644 Dihedral : 4.169 28.025 637 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.62 % Allowed : 9.38 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.00 (0.40), residues: 457 helix: 2.37 (1.68), residues: 11 sheet: 1.84 (0.37), residues: 196 loop : -0.42 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 47 HIS 0.003 0.001 HIS J 66 PHE 0.014 0.002 PHE J 92 TYR 0.020 0.002 TYR J 265 ARG 0.002 0.000 ARG J 237 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.449 Fit side-chains REVERT: J 205 SER cc_start: 0.9190 (p) cc_final: 0.8889 (t) outliers start: 2 outliers final: 1 residues processed: 50 average time/residue: 0.2251 time to fit residues: 13.4113 Evaluate side-chains 48 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 1 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.144131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.113606 restraints weight = 4583.660| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.61 r_work: 0.3109 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 3715 Z= 0.299 Angle : 0.596 6.852 5062 Z= 0.308 Chirality : 0.048 0.202 575 Planarity : 0.004 0.030 644 Dihedral : 4.491 37.072 637 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.25 % Allowed : 9.06 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.79 (0.40), residues: 457 helix: 2.11 (1.75), residues: 11 sheet: 1.83 (0.36), residues: 204 loop : -0.78 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 47 HIS 0.004 0.002 HIS B 35 PHE 0.016 0.002 PHE J 92 TYR 0.022 0.002 TYR J 265 ARG 0.004 0.001 ARG J 237 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.390 Fit side-chains REVERT: A 42 LYS cc_start: 0.8673 (mmmt) cc_final: 0.8375 (mmmm) REVERT: J 205 SER cc_start: 0.9221 (p) cc_final: 0.8892 (t) outliers start: 4 outliers final: 2 residues processed: 47 average time/residue: 0.1976 time to fit residues: 11.2532 Evaluate side-chains 46 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 105 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 23 optimal weight: 0.1980 chunk 8 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 0 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.145725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.114336 restraints weight = 4532.878| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.69 r_work: 0.3109 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3715 Z= 0.222 Angle : 0.534 6.069 5062 Z= 0.277 Chirality : 0.046 0.190 575 Planarity : 0.004 0.031 644 Dihedral : 4.429 38.860 637 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.62 % Allowed : 10.00 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.73 (0.39), residues: 457 helix: 1.97 (1.76), residues: 11 sheet: 1.83 (0.36), residues: 204 loop : -0.87 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 PHE 0.013 0.001 PHE J 92 TYR 0.020 0.001 TYR J 265 ARG 0.002 0.000 ARG J 237 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.351 Fit side-chains REVERT: A 42 LYS cc_start: 0.8625 (mmmt) cc_final: 0.8399 (mmmm) REVERT: J 41 LYS cc_start: 0.7880 (mttt) cc_final: 0.7236 (mtpt) REVERT: J 205 SER cc_start: 0.9207 (p) cc_final: 0.8926 (t) outliers start: 2 outliers final: 1 residues processed: 50 average time/residue: 0.2646 time to fit residues: 15.2844 Evaluate side-chains 47 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 26 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.143696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.113634 restraints weight = 4609.028| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.81 r_work: 0.3059 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 3715 Z= 0.309 Angle : 0.583 6.716 5062 Z= 0.301 Chirality : 0.048 0.203 575 Planarity : 0.004 0.031 644 Dihedral : 4.591 40.445 637 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.25 % Allowed : 9.69 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.57 (0.39), residues: 457 helix: 1.79 (1.76), residues: 11 sheet: 1.70 (0.36), residues: 205 loop : -0.96 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 47 HIS 0.003 0.002 HIS J 66 PHE 0.017 0.002 PHE J 92 TYR 0.022 0.002 TYR J 265 ARG 0.002 0.000 ARG J 237 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.391 Fit side-chains REVERT: A 42 LYS cc_start: 0.8663 (mmmt) cc_final: 0.8450 (mmmm) REVERT: J 41 LYS cc_start: 0.7899 (mttt) cc_final: 0.7254 (mtpt) REVERT: J 205 SER cc_start: 0.9217 (p) cc_final: 0.8893 (t) REVERT: J 304 LYS cc_start: 0.8688 (mmtm) cc_final: 0.8285 (mptt) outliers start: 4 outliers final: 4 residues processed: 50 average time/residue: 0.2507 time to fit residues: 14.6851 Evaluate side-chains 52 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain J residue 227 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 31 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 chunk 44 optimal weight: 0.2980 chunk 13 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 3 optimal weight: 0.0030 chunk 36 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.3790 ------------------------------------------------------------------------------- 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 = 0.3641 r_free = 0.3641 target = 0.145564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.115309 restraints weight = 4487.309| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.61 r_work: 0.3123 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3715 Z= 0.161 Angle : 0.510 5.615 5062 Z= 0.265 Chirality : 0.045 0.187 575 Planarity : 0.003 0.027 644 Dihedral : 4.311 38.501 637 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.62 % Allowed : 10.00 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.71 (0.39), residues: 457 helix: 2.09 (1.77), residues: 11 sheet: 1.78 (0.36), residues: 204 loop : -0.85 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 PHE 0.011 0.001 PHE J 92 TYR 0.020 0.001 TYR J 265 ARG 0.002 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.398 Fit side-chains REVERT: A 42 LYS cc_start: 0.8612 (mmmt) cc_final: 0.8403 (mmmm) REVERT: J 41 LYS cc_start: 0.7871 (mttt) cc_final: 0.7205 (mtpt) REVERT: J 97 LYS cc_start: 0.8836 (ttmm) cc_final: 0.8396 (mtmm) REVERT: J 205 SER cc_start: 0.9212 (p) cc_final: 0.8924 (t) REVERT: J 304 LYS cc_start: 0.8642 (mmtm) cc_final: 0.8264 (mptt) outliers start: 2 outliers final: 2 residues processed: 48 average time/residue: 0.2439 time to fit residues: 13.7559 Evaluate side-chains 47 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 105 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 35 optimal weight: 0.0770 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 41 optimal weight: 0.0070 chunk 40 optimal weight: 0.8980 chunk 34 optimal weight: 0.0470 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 overall best weight: 0.3854 ------------------------------------------------------------------------------- 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 = 0.3644 r_free = 0.3644 target = 0.145742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.115489 restraints weight = 4497.546| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.62 r_work: 0.3138 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3715 Z= 0.166 Angle : 0.509 5.969 5062 Z= 0.264 Chirality : 0.045 0.188 575 Planarity : 0.003 0.030 644 Dihedral : 4.179 37.268 637 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.62 % Allowed : 10.00 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.73 (0.39), residues: 457 helix: 2.13 (1.74), residues: 11 sheet: 1.78 (0.36), residues: 204 loop : -0.82 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 PHE 0.011 0.001 PHE J 92 TYR 0.020 0.001 TYR J 265 ARG 0.002 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.393 Fit side-chains REVERT: A 42 LYS cc_start: 0.8573 (mmmt) cc_final: 0.8351 (mmmm) REVERT: J 41 LYS cc_start: 0.7870 (mttt) cc_final: 0.7189 (mtpt) REVERT: J 205 SER cc_start: 0.9217 (p) cc_final: 0.8946 (t) outliers start: 2 outliers final: 1 residues processed: 47 average time/residue: 0.2358 time to fit residues: 13.0399 Evaluate side-chains 46 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.142778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.112774 restraints weight = 4536.960| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.61 r_work: 0.3086 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 3715 Z= 0.327 Angle : 0.594 6.641 5062 Z= 0.306 Chirality : 0.048 0.207 575 Planarity : 0.004 0.032 644 Dihedral : 4.559 39.892 637 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.31 % Allowed : 10.00 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.47 (0.39), residues: 457 helix: 1.78 (1.75), residues: 11 sheet: 1.60 (0.36), residues: 205 loop : -1.00 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 47 HIS 0.003 0.002 HIS B 35 PHE 0.017 0.002 PHE J 92 TYR 0.023 0.002 TYR J 265 ARG 0.003 0.001 ARG B 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.369 Fit side-chains REVERT: A 42 LYS cc_start: 0.8667 (mmmt) cc_final: 0.8451 (mmmm) REVERT: J 41 LYS cc_start: 0.7925 (mttt) cc_final: 0.7218 (mtpt) REVERT: J 205 SER cc_start: 0.9221 (p) cc_final: 0.8891 (t) outliers start: 1 outliers final: 1 residues processed: 43 average time/residue: 0.2571 time to fit residues: 12.9324 Evaluate side-chains 42 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 28 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 34 optimal weight: 0.2980 chunk 36 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 0.0010 chunk 35 optimal weight: 0.6980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 143 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.144929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.114868 restraints weight = 4523.796| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.62 r_work: 0.3116 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3715 Z= 0.183 Angle : 0.521 6.018 5062 Z= 0.271 Chirality : 0.046 0.189 575 Planarity : 0.004 0.028 644 Dihedral : 4.339 38.793 637 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.31 % Allowed : 9.69 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.57 (0.39), residues: 457 helix: 1.84 (1.74), residues: 11 sheet: 1.76 (0.37), residues: 195 loop : -0.89 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 47 HIS 0.003 0.002 HIS J 143 PHE 0.012 0.001 PHE J 92 TYR 0.020 0.001 TYR J 265 ARG 0.002 0.000 ARG B 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2295.04 seconds wall clock time: 40 minutes 28.48 seconds (2428.48 seconds total)