Starting phenix.real_space_refine on Fri Aug 22 18:09:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8de4_27384/08_2025/8de4_27384.cif Found real_map, /net/cci-nas-00/data/ceres_data/8de4_27384/08_2025/8de4_27384.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8de4_27384/08_2025/8de4_27384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8de4_27384/08_2025/8de4_27384.map" model { file = "/net/cci-nas-00/data/ceres_data/8de4_27384/08_2025/8de4_27384.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8de4_27384/08_2025/8de4_27384.cif" } resolution = 2.9 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= 0.000 sd= 0.025 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 S 35 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 4093 2.51 5 N 957 2.21 5 O 1100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6188 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4298 Classifications: {'peptide': 539} Link IDs: {'PTRANS': 23, 'TRANS': 515} Chain: "B" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "C" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 830 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 103} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 119 Unusual residues: {' CL': 1, ' NA': 2, 'B40': 1, 'LMT': 1, 'Y01': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 1.75, per 1000 atoms: 0.28 Number of scatterers: 6188 At special positions: 0 Unit cell: (79.776, 76.452, 115.509, 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) Cl 1 17.00 S 35 16.00 Na 2 11.00 O 1100 8.00 N 957 7.00 C 4093 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 237 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 115 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 112 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG D 1 " - " ASN A 245 " Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 286.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB B40 A1004 " Number of C-beta restraints generated: 1396 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 7 sheets defined 57.4% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 121 through 134 removed outlier: 4.113A pdb=" N PHE A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 149 Proline residue: A 143 - end of helix Processing helix chain 'A' and resid 154 through 181 removed outlier: 5.015A pdb=" N ILE A 167 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 196 through 227 removed outlier: 4.132A pdb=" N PHE A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 272 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 289 through 307 Processing helix chain 'A' and resid 310 through 322 removed outlier: 3.808A pdb=" N SER A 314 " --> pdb=" O GLY A 310 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL A 320 " --> pdb=" O LYS A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 337 Processing helix chain 'A' and resid 341 through 350 removed outlier: 3.775A pdb=" N GLY A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 358 Processing helix chain 'A' and resid 359 through 375 removed outlier: 4.215A pdb=" N TRP A 363 " --> pdb=" O GLU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 387 removed outlier: 3.864A pdb=" N ALA A 383 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 428 removed outlier: 3.801A pdb=" N ASP A 397 " --> pdb=" O ASN A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 454 removed outlier: 4.524A pdb=" N ALA A 448 " --> pdb=" O PHE A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 491 Processing helix chain 'A' and resid 492 through 495 removed outlier: 3.699A pdb=" N TRP A 495 " --> pdb=" O PRO A 492 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 492 through 495' Processing helix chain 'A' and resid 497 through 518 removed outlier: 4.014A pdb=" N TRP A 501 " --> pdb=" O LYS A 497 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N THR A 517 " --> pdb=" O GLY A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 532 removed outlier: 4.453A pdb=" N VAL A 525 " --> pdb=" O GLY A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 552 Processing helix chain 'A' and resid 554 through 567 Processing helix chain 'A' and resid 571 through 595 removed outlier: 4.275A pdb=" N VAL A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N SER A 582 " --> pdb=" O TRP A 578 " (cutoff:3.500A) Proline residue: A 583 - end of helix Processing helix chain 'A' and resid 608 through 624 removed outlier: 3.638A pdb=" N ILE A 612 " --> pdb=" O PRO A 608 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER A 622 " --> pdb=" O ILE A 618 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE A 623 " --> pdb=" O GLY A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 637 removed outlier: 4.279A pdb=" N THR A 637 " --> pdb=" O ARG A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 650 Processing helix chain 'B' and resid 47 through 51 removed outlier: 4.028A pdb=" N SER B 51 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 106 through 110 Processing helix chain 'C' and resid 103 through 107 removed outlier: 3.544A pdb=" N ASP C 106 " --> pdb=" O GLU C 103 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 601 through 602 removed outlier: 3.508A pdb=" N TYR A 605 " --> pdb=" O LEU A 602 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 22 through 25 Processing sheet with id=AA3, first strand: chain 'B' and resid 37 through 39 removed outlier: 3.640A pdb=" N ILE B 39 " --> pdb=" O MET B 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 77 through 79 removed outlier: 6.550A pdb=" N TRP B 55 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG B 69 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N MET B 53 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR B 129 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 77 through 79 removed outlier: 6.550A pdb=" N TRP B 55 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG B 69 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N MET B 53 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 24 through 27 Processing sheet with id=AA7, first strand: chain 'C' and resid 30 through 32 removed outlier: 7.002A pdb=" N LEU C 31 " --> pdb=" O GLU C 129 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE C 111 " --> pdb=" O PHE C 60 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU C 57 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TYR C 73 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TRP C 59 " --> pdb=" O LEU C 71 " (cutoff:3.500A) 355 hydrogen bonds defined for protein. 1005 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: 1.09 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 924 1.31 - 1.44: 1933 1.44 - 1.56: 3443 1.56 - 1.69: 21 1.69 - 1.81: 53 Bond restraints: 6374 Sorted by residual: bond pdb=" CAI Y01 A1005 " pdb=" CAZ Y01 A1005 " ideal model delta sigma weight residual 1.332 1.556 -0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" CAI Y01 A1006 " pdb=" CAZ Y01 A1006 " ideal model delta sigma weight residual 1.332 1.547 -0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" CAU Y01 A1006 " pdb=" CBI Y01 A1006 " ideal model delta sigma weight residual 1.530 1.721 -0.191 2.00e-02 2.50e+03 9.14e+01 bond pdb=" CAU Y01 A1005 " pdb=" CBI Y01 A1005 " ideal model delta sigma weight residual 1.530 1.719 -0.189 2.00e-02 2.50e+03 8.97e+01 bond pdb=" CAP Y01 A1005 " pdb=" CBE Y01 A1005 " ideal model delta sigma weight residual 1.553 1.386 0.167 2.00e-02 2.50e+03 7.01e+01 ... (remaining 6369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.63: 8621 3.63 - 7.26: 44 7.26 - 10.90: 16 10.90 - 14.53: 5 14.53 - 18.16: 1 Bond angle restraints: 8687 Sorted by residual: angle pdb=" CA PRO A 570 " pdb=" N PRO A 570 " pdb=" CD PRO A 570 " ideal model delta sigma weight residual 112.00 93.84 18.16 1.40e+00 5.10e-01 1.68e+02 angle pdb=" N PRO A 570 " pdb=" CD PRO A 570 " pdb=" CG PRO A 570 " ideal model delta sigma weight residual 103.20 91.96 11.24 1.50e+00 4.44e-01 5.62e+01 angle pdb=" CA PRO A 570 " pdb=" CB PRO A 570 " pdb=" CG PRO A 570 " ideal model delta sigma weight residual 104.50 95.67 8.83 1.90e+00 2.77e-01 2.16e+01 angle pdb=" CAK Y01 A1006 " pdb=" CAI Y01 A1006 " pdb=" CAZ Y01 A1006 " ideal model delta sigma weight residual 124.96 111.15 13.81 3.00e+00 1.11e-01 2.12e+01 angle pdb=" CAI Y01 A1006 " pdb=" CAZ Y01 A1006 " pdb=" CBH Y01 A1006 " ideal model delta sigma weight residual 123.00 110.66 12.34 3.00e+00 1.11e-01 1.69e+01 ... (remaining 8682 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.50: 3319 21.50 - 42.99: 386 42.99 - 64.49: 74 64.49 - 85.98: 5 85.98 - 107.48: 8 Dihedral angle restraints: 3792 sinusoidal: 1593 harmonic: 2199 Sorted by residual: dihedral pdb=" CAU Y01 A1006 " pdb=" CAS Y01 A1006 " pdb=" CBF Y01 A1006 " pdb=" CBD Y01 A1006 " ideal model delta sinusoidal sigma weight residual 50.87 -56.61 107.48 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" CAU Y01 A1006 " pdb=" CBE Y01 A1006 " pdb=" CBI Y01 A1006 " pdb=" CBB Y01 A1006 " ideal model delta sinusoidal sigma weight residual -81.21 20.96 -102.17 1 3.00e+01 1.11e-03 1.29e+01 dihedral pdb=" CAS Y01 A1006 " pdb=" CBF Y01 A1006 " pdb=" CBH Y01 A1006 " pdb=" CAT Y01 A1006 " ideal model delta sinusoidal sigma weight residual 68.57 -29.00 97.57 1 3.00e+01 1.11e-03 1.21e+01 ... (remaining 3789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.017: 967 1.017 - 2.034: 0 2.034 - 3.051: 0 3.051 - 4.068: 0 4.068 - 5.086: 2 Chirality restraints: 969 Sorted by residual: chirality pdb=" CBE Y01 A1006 " pdb=" CAP Y01 A1006 " pdb=" CBB Y01 A1006 " pdb=" CBI Y01 A1006 " both_signs ideal model delta sigma weight residual False 2.57 -2.52 5.09 2.00e-01 2.50e+01 6.47e+02 chirality pdb=" CBF Y01 A1006 " pdb=" CAS Y01 A1006 " pdb=" CBD Y01 A1006 " pdb=" CBH Y01 A1006 " both_signs ideal model delta sigma weight residual False -2.45 2.30 -4.74 2.00e-01 2.50e+01 5.62e+02 chirality pdb=" CBG Y01 A1005 " pdb=" CAQ Y01 A1005 " pdb=" CBD Y01 A1005 " pdb=" CBI Y01 A1005 " both_signs ideal model delta sigma weight residual False -2.33 -2.79 0.46 2.00e-01 2.50e+01 5.21e+00 ... (remaining 966 not shown) Planarity restraints: 1053 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 569 " -0.112 5.00e-02 4.00e+02 1.53e-01 3.75e+01 pdb=" N PRO A 570 " 0.264 5.00e-02 4.00e+02 pdb=" CA PRO A 570 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO A 570 " -0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 454 " -0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO A 455 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 455 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 455 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 477 " -0.009 2.00e-02 2.50e+03 9.43e-03 1.56e+00 pdb=" CG PHE A 477 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE A 477 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 477 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 477 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 477 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 477 " -0.000 2.00e-02 2.50e+03 ... (remaining 1050 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 89 2.66 - 3.22: 5688 3.22 - 3.78: 10067 3.78 - 4.34: 13654 4.34 - 4.90: 22514 Nonbonded interactions: 52012 Sorted by model distance: nonbonded pdb=" OG SER A 596 " pdb=" O6' LMT A1007 " model vdw 2.096 3.040 nonbonded pdb=" O GLY A 639 " pdb=" NH2 ARG A 644 " model vdw 2.242 3.120 nonbonded pdb=" N ASP B 128 " pdb=" OD1 ASP B 128 " model vdw 2.270 3.120 nonbonded pdb=" O TYR A 223 " pdb=" OG SER A 227 " model vdw 2.325 3.040 nonbonded pdb=" OG SER A 263 " pdb=" OE2 GLU A 449 " model vdw 2.327 3.040 ... (remaining 52007 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: 3.200 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.070 Find NCS groups from input model: 0.040 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:7.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6418 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 : 0.009 0.224 6379 Z= 0.434 Angle : 0.790 18.160 8699 Z= 0.371 Chirality : 0.228 5.086 969 Planarity : 0.005 0.153 1052 Dihedral : 18.019 107.481 2387 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.35 % Allowed : 30.12 % Favored : 65.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.28 (0.32), residues: 761 helix: 1.23 (0.27), residues: 375 sheet: -0.49 (0.54), residues: 111 loop : -0.92 (0.40), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 335 TYR 0.016 0.001 TYR A 213 PHE 0.020 0.001 PHE A 477 TRP 0.008 0.001 TRP A 572 HIS 0.001 0.000 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00886 ( 6374) covalent geometry : angle 0.78860 ( 8687) SS BOND : bond 0.00071 ( 3) SS BOND : angle 0.28213 ( 6) hydrogen bonds : bond 0.15965 ( 344) hydrogen bonds : angle 6.47818 ( 1005) link_BETA1-4 : bond 0.00412 ( 1) link_BETA1-4 : angle 1.81337 ( 3) link_NAG-ASN : bond 0.00774 ( 1) link_NAG-ASN : angle 2.38275 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 64 time to evaluate : 0.229 Fit side-chains outliers start: 28 outliers final: 26 residues processed: 92 average time/residue: 0.3339 time to fit residues: 33.4370 Evaluate side-chains 87 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 61 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 80 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.187474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.164057 restraints weight = 6598.067| |-----------------------------------------------------------------------------| r_work (start): 0.4197 rms_B_bonded: 1.73 r_work: 0.4121 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4011 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 6379 Z= 0.163 Angle : 0.569 6.614 8699 Z= 0.289 Chirality : 0.042 0.263 969 Planarity : 0.004 0.069 1052 Dihedral : 10.311 59.921 1112 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 6.06 % Allowed : 26.71 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.00 (0.31), residues: 761 helix: 0.88 (0.26), residues: 380 sheet: -0.47 (0.53), residues: 104 loop : -0.94 (0.40), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 271 TYR 0.012 0.001 TYR A 304 PHE 0.020 0.002 PHE A 585 TRP 0.014 0.001 TRP B 66 HIS 0.002 0.001 HIS A 272 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 6374) covalent geometry : angle 0.56665 ( 8687) SS BOND : bond 0.00437 ( 3) SS BOND : angle 0.80391 ( 6) hydrogen bonds : bond 0.04460 ( 344) hydrogen bonds : angle 5.03362 ( 1005) link_BETA1-4 : bond 0.00108 ( 1) link_BETA1-4 : angle 0.97444 ( 3) link_NAG-ASN : bond 0.00168 ( 1) link_NAG-ASN : angle 2.46010 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 61 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 217 MET cc_start: 0.6057 (mmm) cc_final: 0.5621 (mmm) REVERT: A 407 MET cc_start: 0.5912 (OUTLIER) cc_final: 0.5609 (mmm) REVERT: A 414 PHE cc_start: 0.5540 (OUTLIER) cc_final: 0.5314 (m-10) REVERT: A 518 LEU cc_start: 0.6283 (tp) cc_final: 0.5946 (mt) REVERT: A 643 GLU cc_start: 0.6496 (OUTLIER) cc_final: 0.5389 (pm20) outliers start: 39 outliers final: 23 residues processed: 93 average time/residue: 0.3620 time to fit residues: 36.5210 Evaluate side-chains 87 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 61 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 643 GLU Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 102 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 30 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4418 r_free = 0.4418 target = 0.187645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.165025 restraints weight = 6623.016| |-----------------------------------------------------------------------------| r_work (start): 0.4207 rms_B_bonded: 1.73 r_work: 0.4129 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.4016 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6379 Z= 0.154 Angle : 0.548 6.461 8699 Z= 0.280 Chirality : 0.041 0.282 969 Planarity : 0.004 0.051 1052 Dihedral : 9.360 58.409 1092 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 6.37 % Allowed : 27.64 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.31), residues: 761 helix: 0.66 (0.26), residues: 379 sheet: -0.43 (0.52), residues: 104 loop : -1.10 (0.40), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 271 TYR 0.013 0.001 TYR A 629 PHE 0.018 0.002 PHE A 585 TRP 0.015 0.001 TRP B 66 HIS 0.001 0.000 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 6374) covalent geometry : angle 0.54605 ( 8687) SS BOND : bond 0.00459 ( 3) SS BOND : angle 0.76285 ( 6) hydrogen bonds : bond 0.04610 ( 344) hydrogen bonds : angle 4.91849 ( 1005) link_BETA1-4 : bond 0.00366 ( 1) link_BETA1-4 : angle 0.59721 ( 3) link_NAG-ASN : bond 0.00331 ( 1) link_NAG-ASN : angle 2.32004 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 65 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 407 MET cc_start: 0.6130 (OUTLIER) cc_final: 0.5808 (mmm) REVERT: A 518 LEU cc_start: 0.6505 (tp) cc_final: 0.6241 (mt) REVERT: A 643 GLU cc_start: 0.6295 (OUTLIER) cc_final: 0.5636 (pm20) REVERT: B 47 ARG cc_start: 0.7410 (mtm180) cc_final: 0.7172 (mtp180) REVERT: C 129 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7037 (mt-10) outliers start: 41 outliers final: 28 residues processed: 97 average time/residue: 0.3120 time to fit residues: 33.1062 Evaluate side-chains 94 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 64 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 643 GLU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 102 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 30 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 = 0.4368 r_free = 0.4368 target = 0.183985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.160490 restraints weight = 6615.736| |-----------------------------------------------------------------------------| r_work (start): 0.4144 rms_B_bonded: 1.74 r_work: 0.4067 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3957 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6379 Z= 0.156 Angle : 0.561 6.749 8699 Z= 0.286 Chirality : 0.041 0.275 969 Planarity : 0.004 0.045 1052 Dihedral : 9.072 58.316 1090 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 6.06 % Allowed : 27.64 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.39 (0.31), residues: 761 helix: 0.57 (0.26), residues: 383 sheet: -0.35 (0.53), residues: 104 loop : -1.31 (0.40), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 271 TYR 0.016 0.001 TYR A 387 PHE 0.018 0.002 PHE A 585 TRP 0.016 0.001 TRP B 66 HIS 0.001 0.000 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 6374) covalent geometry : angle 0.55868 ( 8687) SS BOND : bond 0.00495 ( 3) SS BOND : angle 0.86841 ( 6) hydrogen bonds : bond 0.04521 ( 344) hydrogen bonds : angle 4.88305 ( 1005) link_BETA1-4 : bond 0.00369 ( 1) link_BETA1-4 : angle 0.61401 ( 3) link_NAG-ASN : bond 0.00298 ( 1) link_NAG-ASN : angle 2.31534 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 70 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 407 MET cc_start: 0.6145 (OUTLIER) cc_final: 0.5898 (mmp) REVERT: A 643 GLU cc_start: 0.6377 (OUTLIER) cc_final: 0.5218 (pm20) REVERT: B 47 ARG cc_start: 0.7397 (mtm180) cc_final: 0.7156 (mtp180) REVERT: B 74 ASP cc_start: 0.8024 (m-30) cc_final: 0.7725 (m-30) REVERT: B 97 THR cc_start: 0.7426 (OUTLIER) cc_final: 0.7151 (t) REVERT: C 129 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7062 (mt-10) outliers start: 39 outliers final: 25 residues processed: 99 average time/residue: 0.3380 time to fit residues: 36.5278 Evaluate side-chains 96 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 68 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 632 TYR Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 643 GLU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 102 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 47 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 26 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 113 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.188286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.167083 restraints weight = 6687.053| |-----------------------------------------------------------------------------| r_work (start): 0.4231 rms_B_bonded: 1.63 r_work: 0.4157 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.4052 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6379 Z= 0.133 Angle : 0.536 6.133 8699 Z= 0.276 Chirality : 0.040 0.247 969 Planarity : 0.004 0.042 1052 Dihedral : 8.716 57.979 1088 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 7.30 % Allowed : 27.17 % Favored : 65.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.28 (0.31), residues: 761 helix: 0.64 (0.26), residues: 384 sheet: -0.22 (0.53), residues: 104 loop : -1.27 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 644 TYR 0.015 0.001 TYR A 387 PHE 0.015 0.001 PHE A 585 TRP 0.015 0.001 TRP B 66 HIS 0.001 0.000 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 6374) covalent geometry : angle 0.53422 ( 8687) SS BOND : bond 0.00387 ( 3) SS BOND : angle 0.70388 ( 6) hydrogen bonds : bond 0.04258 ( 344) hydrogen bonds : angle 4.78391 ( 1005) link_BETA1-4 : bond 0.00338 ( 1) link_BETA1-4 : angle 0.69931 ( 3) link_NAG-ASN : bond 0.00433 ( 1) link_NAG-ASN : angle 2.26613 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 66 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 217 MET cc_start: 0.5949 (mtp) cc_final: 0.5617 (mtp) REVERT: A 414 PHE cc_start: 0.5875 (OUTLIER) cc_final: 0.5585 (m-10) REVERT: A 643 GLU cc_start: 0.6298 (OUTLIER) cc_final: 0.5133 (pm20) REVERT: B 74 ASP cc_start: 0.8037 (m-30) cc_final: 0.7764 (m-30) REVERT: C 129 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7153 (mt-10) outliers start: 47 outliers final: 33 residues processed: 105 average time/residue: 0.3100 time to fit residues: 35.5673 Evaluate side-chains 100 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 65 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 632 TYR Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 643 GLU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 102 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 31 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 10 optimal weight: 0.3980 chunk 12 optimal weight: 0.9980 chunk 14 optimal weight: 0.0030 chunk 37 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 overall best weight: 0.3590 ------------------------------------------------------------------------------- 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 = 0.4440 r_free = 0.4440 target = 0.190432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.169435 restraints weight = 6491.394| |-----------------------------------------------------------------------------| r_work (start): 0.4256 rms_B_bonded: 1.58 r_work: 0.4192 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.4092 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6379 Z= 0.115 Angle : 0.515 6.039 8699 Z= 0.265 Chirality : 0.039 0.223 969 Planarity : 0.003 0.039 1052 Dihedral : 8.285 58.020 1088 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 5.75 % Allowed : 27.64 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.11 (0.31), residues: 761 helix: 0.76 (0.26), residues: 384 sheet: -0.03 (0.54), residues: 104 loop : -1.22 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 644 TYR 0.015 0.001 TYR A 387 PHE 0.013 0.001 PHE A 585 TRP 0.013 0.001 TRP B 66 HIS 0.001 0.001 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 6374) covalent geometry : angle 0.51305 ( 8687) SS BOND : bond 0.00344 ( 3) SS BOND : angle 0.78386 ( 6) hydrogen bonds : bond 0.03998 ( 344) hydrogen bonds : angle 4.65040 ( 1005) link_BETA1-4 : bond 0.00405 ( 1) link_BETA1-4 : angle 0.85821 ( 3) link_NAG-ASN : bond 0.00507 ( 1) link_NAG-ASN : angle 2.29037 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 71 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 258 MET cc_start: 0.5513 (mpp) cc_final: 0.2630 (ttp) REVERT: A 414 PHE cc_start: 0.5853 (OUTLIER) cc_final: 0.5554 (m-10) REVERT: A 585 PHE cc_start: 0.6297 (OUTLIER) cc_final: 0.6092 (p90) REVERT: A 643 GLU cc_start: 0.6183 (OUTLIER) cc_final: 0.4970 (pm20) REVERT: B 42 LYS cc_start: 0.6890 (OUTLIER) cc_final: 0.6483 (tttt) REVERT: B 74 ASP cc_start: 0.7872 (m-30) cc_final: 0.7622 (m-30) REVERT: C 129 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7148 (mt-10) outliers start: 37 outliers final: 24 residues processed: 101 average time/residue: 0.3624 time to fit residues: 39.8061 Evaluate side-chains 96 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 68 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 643 GLU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 102 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 14 optimal weight: 0.4980 chunk 47 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 57 optimal weight: 0.0570 chunk 38 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.190126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.167556 restraints weight = 6551.529| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 1.72 r_work: 0.4174 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.4066 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6379 Z= 0.118 Angle : 0.525 7.215 8699 Z= 0.268 Chirality : 0.039 0.232 969 Planarity : 0.003 0.038 1052 Dihedral : 7.922 59.124 1088 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 5.59 % Allowed : 28.42 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.16 (0.31), residues: 761 helix: 0.76 (0.26), residues: 386 sheet: 0.09 (0.53), residues: 104 loop : -1.40 (0.40), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 181 TYR 0.015 0.001 TYR A 387 PHE 0.015 0.001 PHE A 477 TRP 0.014 0.001 TRP B 66 HIS 0.001 0.000 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 6374) covalent geometry : angle 0.52238 ( 8687) SS BOND : bond 0.00315 ( 3) SS BOND : angle 1.00347 ( 6) hydrogen bonds : bond 0.03995 ( 344) hydrogen bonds : angle 4.61222 ( 1005) link_BETA1-4 : bond 0.00359 ( 1) link_BETA1-4 : angle 0.83598 ( 3) link_NAG-ASN : bond 0.00437 ( 1) link_NAG-ASN : angle 2.28489 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 70 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 414 PHE cc_start: 0.5930 (OUTLIER) cc_final: 0.5642 (m-10) REVERT: A 585 PHE cc_start: 0.6335 (OUTLIER) cc_final: 0.6116 (p90) REVERT: A 643 GLU cc_start: 0.6224 (OUTLIER) cc_final: 0.4977 (pm20) REVERT: B 42 LYS cc_start: 0.7053 (OUTLIER) cc_final: 0.6667 (tttt) REVERT: B 74 ASP cc_start: 0.7903 (m-30) cc_final: 0.7650 (m-30) outliers start: 36 outliers final: 28 residues processed: 98 average time/residue: 0.3195 time to fit residues: 34.1799 Evaluate side-chains 102 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 70 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 643 GLU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 102 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 4 optimal weight: 0.5980 chunk 64 optimal weight: 0.4980 chunk 2 optimal weight: 0.0970 chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 70 optimal weight: 0.0870 chunk 10 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 overall best weight: 0.3756 ------------------------------------------------------------------------------- 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 = 0.4443 r_free = 0.4443 target = 0.190881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.170049 restraints weight = 6509.179| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 1.58 r_work: 0.4202 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.4100 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6379 Z= 0.116 Angle : 0.523 6.446 8699 Z= 0.267 Chirality : 0.039 0.226 969 Planarity : 0.003 0.038 1052 Dihedral : 7.674 59.788 1087 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 5.59 % Allowed : 28.73 % Favored : 65.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.13 (0.31), residues: 761 helix: 0.78 (0.26), residues: 386 sheet: 0.15 (0.54), residues: 104 loop : -1.40 (0.40), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 181 TYR 0.015 0.001 TYR A 387 PHE 0.019 0.001 PHE A 477 TRP 0.016 0.001 TRP B 66 HIS 0.001 0.000 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 6374) covalent geometry : angle 0.52140 ( 8687) SS BOND : bond 0.00311 ( 3) SS BOND : angle 0.83413 ( 6) hydrogen bonds : bond 0.03961 ( 344) hydrogen bonds : angle 4.57333 ( 1005) link_BETA1-4 : bond 0.00404 ( 1) link_BETA1-4 : angle 0.86870 ( 3) link_NAG-ASN : bond 0.00502 ( 1) link_NAG-ASN : angle 2.28815 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 71 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 258 MET cc_start: 0.5418 (mpp) cc_final: 0.2560 (ttp) REVERT: A 414 PHE cc_start: 0.5916 (OUTLIER) cc_final: 0.5633 (m-10) REVERT: A 643 GLU cc_start: 0.6026 (OUTLIER) cc_final: 0.4809 (pm20) REVERT: B 42 LYS cc_start: 0.6994 (OUTLIER) cc_final: 0.6602 (tttt) REVERT: B 74 ASP cc_start: 0.7899 (m-30) cc_final: 0.7680 (m-30) outliers start: 36 outliers final: 25 residues processed: 99 average time/residue: 0.3216 time to fit residues: 34.9139 Evaluate side-chains 97 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 69 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 643 GLU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 102 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 55 optimal weight: 0.2980 chunk 40 optimal weight: 0.0170 chunk 7 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 2 optimal weight: 0.0770 chunk 4 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 overall best weight: 0.3776 ------------------------------------------------------------------------------- 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 = 0.4447 r_free = 0.4447 target = 0.191130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.170084 restraints weight = 6516.579| |-----------------------------------------------------------------------------| r_work (start): 0.4264 rms_B_bonded: 1.61 r_work: 0.4202 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.4100 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6379 Z= 0.117 Angle : 0.526 5.971 8699 Z= 0.268 Chirality : 0.039 0.260 969 Planarity : 0.003 0.037 1052 Dihedral : 7.376 59.656 1085 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.97 % Allowed : 29.81 % Favored : 65.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.14 (0.31), residues: 761 helix: 0.76 (0.26), residues: 386 sheet: 0.16 (0.54), residues: 104 loop : -1.38 (0.40), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 181 TYR 0.016 0.001 TYR A 387 PHE 0.024 0.001 PHE A 477 TRP 0.016 0.001 TRP A 234 HIS 0.002 0.000 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 6374) covalent geometry : angle 0.52368 ( 8687) SS BOND : bond 0.00297 ( 3) SS BOND : angle 0.83266 ( 6) hydrogen bonds : bond 0.03988 ( 344) hydrogen bonds : angle 4.56433 ( 1005) link_BETA1-4 : bond 0.00379 ( 1) link_BETA1-4 : angle 0.86655 ( 3) link_NAG-ASN : bond 0.00467 ( 1) link_NAG-ASN : angle 2.28516 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 68 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 258 MET cc_start: 0.5447 (mpp) cc_final: 0.2576 (ttp) REVERT: A 414 PHE cc_start: 0.5906 (OUTLIER) cc_final: 0.5621 (m-10) REVERT: A 643 GLU cc_start: 0.6044 (OUTLIER) cc_final: 0.4784 (pm20) REVERT: B 42 LYS cc_start: 0.6998 (OUTLIER) cc_final: 0.6632 (tttt) REVERT: B 74 ASP cc_start: 0.7896 (m-30) cc_final: 0.7675 (m-30) outliers start: 32 outliers final: 26 residues processed: 94 average time/residue: 0.3430 time to fit residues: 35.1418 Evaluate side-chains 97 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 68 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 643 GLU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 102 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 14 optimal weight: 0.0870 chunk 0 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.186569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.164339 restraints weight = 6474.010| |-----------------------------------------------------------------------------| r_work (start): 0.4197 rms_B_bonded: 1.67 r_work: 0.4123 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.4013 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6379 Z= 0.141 Angle : 0.557 6.226 8699 Z= 0.285 Chirality : 0.041 0.264 969 Planarity : 0.003 0.039 1052 Dihedral : 7.394 58.797 1085 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 5.12 % Allowed : 29.97 % Favored : 64.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.31), residues: 761 helix: 0.62 (0.26), residues: 385 sheet: 0.20 (0.55), residues: 102 loop : -1.37 (0.40), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 181 TYR 0.018 0.001 TYR A 387 PHE 0.029 0.002 PHE A 477 TRP 0.018 0.001 TRP A 234 HIS 0.001 0.000 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 6374) covalent geometry : angle 0.55529 ( 8687) SS BOND : bond 0.00431 ( 3) SS BOND : angle 1.01855 ( 6) hydrogen bonds : bond 0.04273 ( 344) hydrogen bonds : angle 4.66634 ( 1005) link_BETA1-4 : bond 0.00418 ( 1) link_BETA1-4 : angle 0.75754 ( 3) link_NAG-ASN : bond 0.00345 ( 1) link_NAG-ASN : angle 2.37393 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 69 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 414 PHE cc_start: 0.5856 (OUTLIER) cc_final: 0.5544 (m-10) REVERT: A 643 GLU cc_start: 0.6323 (OUTLIER) cc_final: 0.5103 (pm20) REVERT: B 42 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.6582 (tttt) REVERT: B 74 ASP cc_start: 0.7929 (m-30) cc_final: 0.7652 (m-30) outliers start: 33 outliers final: 28 residues processed: 96 average time/residue: 0.3282 time to fit residues: 34.5109 Evaluate side-chains 99 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 68 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 632 TYR Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 643 GLU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 102 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 53 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 68 optimal weight: 0.0770 chunk 29 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 52 optimal weight: 0.0980 chunk 45 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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 = 0.4421 r_free = 0.4421 target = 0.188226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.165389 restraints weight = 6629.349| |-----------------------------------------------------------------------------| r_work (start): 0.4227 rms_B_bonded: 1.74 r_work: 0.4157 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.4052 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6379 Z= 0.126 Angle : 0.542 6.849 8699 Z= 0.276 Chirality : 0.040 0.233 969 Planarity : 0.003 0.039 1052 Dihedral : 7.316 59.993 1085 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 5.28 % Allowed : 29.97 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.18 (0.31), residues: 761 helix: 0.64 (0.26), residues: 388 sheet: 0.27 (0.55), residues: 102 loop : -1.30 (0.40), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 181 TYR 0.015 0.001 TYR A 387 PHE 0.026 0.001 PHE A 477 TRP 0.019 0.001 TRP A 234 HIS 0.002 0.000 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 6374) covalent geometry : angle 0.53999 ( 8687) SS BOND : bond 0.00361 ( 3) SS BOND : angle 0.91409 ( 6) hydrogen bonds : bond 0.04097 ( 344) hydrogen bonds : angle 4.62452 ( 1005) link_BETA1-4 : bond 0.00410 ( 1) link_BETA1-4 : angle 0.83541 ( 3) link_NAG-ASN : bond 0.00474 ( 1) link_NAG-ASN : angle 2.31182 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2454.89 seconds wall clock time: 42 minutes 53.51 seconds (2573.51 seconds total)