Starting phenix.real_space_refine on Thu Jul 24 22:12:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8de4_27384/07_2025/8de4_27384.cif Found real_map, /net/cci-nas-00/data/ceres_data/8de4_27384/07_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_27384/07_2025/8de4_27384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8de4_27384/07_2025/8de4_27384.map" model { file = "/net/cci-nas-00/data/ceres_data/8de4_27384/07_2025/8de4_27384.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8de4_27384/07_2025/8de4_27384.cif" } resolution = 2.9 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= 0.025 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 4.92, per 1000 atoms: 0.80 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: 1.66 Conformation dependent library (CDL) restraints added in 845.3 milliseconds 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: 0.66 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: 1.71 Time building geometry restraints manager: 1.93 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: 2.750 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: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.900 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.070 ------------------------------------------------------------------------------- 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 (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: 0.28 (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 TRP 0.008 0.001 TRP A 572 HIS 0.001 0.000 HIS A 180 PHE 0.020 0.001 PHE A 477 TYR 0.016 0.001 TYR A 213 ARG 0.001 0.000 ARG A 335 Details of bonding type rmsd link_NAG-ASN : bond 0.00774 ( 1) link_NAG-ASN : angle 2.38275 ( 3) link_BETA1-4 : bond 0.00412 ( 1) link_BETA1-4 : angle 1.81337 ( 3) hydrogen bonds : bond 0.15965 ( 344) hydrogen bonds : angle 6.47818 ( 1005) SS BOND : bond 0.00071 ( 3) SS BOND : angle 0.28213 ( 6) covalent geometry : bond 0.00886 ( 6374) covalent geometry : angle 0.78860 ( 8687) *********************** 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 : 0.619 Fit side-chains outliers start: 28 outliers final: 26 residues processed: 92 average time/residue: 0.6887 time to fit residues: 69.2580 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 : 0.626 ------------------------------------------------------------------------------- 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 63 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 58 optimal weight: 0.0870 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 0.0980 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 = 0.4448 r_free = 0.4448 target = 0.192281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.169004 restraints weight = 6389.855| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 1.74 r_work: 0.4170 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4060 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 6379 Z= 0.130 Angle : 0.535 6.928 8699 Z= 0.270 Chirality : 0.040 0.225 969 Planarity : 0.004 0.074 1052 Dihedral : 10.238 59.486 1112 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 5.75 % Allowed : 26.55 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.16 (0.31), residues: 761 helix: 1.08 (0.26), residues: 379 sheet: -0.44 (0.53), residues: 104 loop : -0.94 (0.40), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 66 HIS 0.001 0.000 HIS A 272 PHE 0.017 0.001 PHE A 585 TYR 0.010 0.001 TYR A 304 ARG 0.004 0.000 ARG A 271 Details of bonding type rmsd link_NAG-ASN : bond 0.00346 ( 1) link_NAG-ASN : angle 2.32476 ( 3) link_BETA1-4 : bond 0.00143 ( 1) link_BETA1-4 : angle 0.90358 ( 3) hydrogen bonds : bond 0.04223 ( 344) hydrogen bonds : angle 4.97410 ( 1005) SS BOND : bond 0.00308 ( 3) SS BOND : angle 0.60267 ( 6) covalent geometry : bond 0.00295 ( 6374) covalent geometry : angle 0.53320 ( 8687) *********************** 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: 37 poor density : 63 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.5772 (OUTLIER) cc_final: 0.5482 (mmm) REVERT: A 414 PHE cc_start: 0.5605 (OUTLIER) cc_final: 0.5388 (m-10) REVERT: A 518 LEU cc_start: 0.6094 (tp) cc_final: 0.5739 (mt) REVERT: A 643 GLU cc_start: 0.6418 (OUTLIER) cc_final: 0.5325 (pm20) REVERT: B 47 ARG cc_start: 0.7226 (mtm180) cc_final: 0.6966 (mtp180) outliers start: 37 outliers final: 19 residues processed: 93 average time/residue: 0.7061 time to fit residues: 71.4842 Evaluate side-chains 84 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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 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 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 C residue 57 LEU 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 49 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 26 optimal weight: 0.0470 chunk 15 optimal weight: 0.8980 chunk 71 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 overall best weight: 0.4678 ------------------------------------------------------------------------------- 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 = 0.4469 r_free = 0.4469 target = 0.193275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.173105 restraints weight = 6438.405| |-----------------------------------------------------------------------------| r_work (start): 0.4293 rms_B_bonded: 1.53 r_work: 0.4234 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.4135 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.1309 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= 0.124 Angle : 0.509 5.786 8699 Z= 0.260 Chirality : 0.039 0.246 969 Planarity : 0.004 0.048 1052 Dihedral : 9.005 58.044 1092 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 5.59 % Allowed : 27.17 % 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 (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: 0.06 (0.31), residues: 761 helix: 0.96 (0.26), residues: 380 sheet: -0.38 (0.52), residues: 104 loop : -1.02 (0.40), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 66 HIS 0.001 0.000 HIS A 277 PHE 0.015 0.001 PHE A 585 TYR 0.011 0.001 TYR A 387 ARG 0.003 0.000 ARG A 271 Details of bonding type rmsd link_NAG-ASN : bond 0.00382 ( 1) link_NAG-ASN : angle 2.16423 ( 3) link_BETA1-4 : bond 0.00307 ( 1) link_BETA1-4 : angle 0.71033 ( 3) hydrogen bonds : bond 0.04134 ( 344) hydrogen bonds : angle 4.73458 ( 1005) SS BOND : bond 0.00315 ( 3) SS BOND : angle 0.58647 ( 6) covalent geometry : bond 0.00274 ( 6374) covalent geometry : angle 0.50756 ( 8687) *********************** 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 100 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 64 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: A 217 MET cc_start: 0.6122 (mmm) cc_final: 0.5780 (mmm) REVERT: A 407 MET cc_start: 0.6128 (OUTLIER) cc_final: 0.5789 (mmm) REVERT: A 518 LEU cc_start: 0.6285 (tp) cc_final: 0.6007 (mt) REVERT: A 643 GLU cc_start: 0.6129 (OUTLIER) cc_final: 0.5155 (pm20) REVERT: B 74 ASP cc_start: 0.8043 (m-30) cc_final: 0.7760 (m-30) REVERT: B 97 THR cc_start: 0.7326 (OUTLIER) cc_final: 0.7024 (t) outliers start: 36 outliers final: 23 residues processed: 92 average time/residue: 0.7599 time to fit residues: 76.3718 Evaluate side-chains 89 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 63 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 MET 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 305 PHE Chi-restraints excluded: chain A residue 311 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 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 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 97 THR Chi-restraints excluded: chain C residue 54 ILE 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 37 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 71 optimal weight: 0.0980 chunk 46 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 13 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4366 r_free = 0.4366 target = 0.183659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.160011 restraints weight = 6654.388| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 1.74 r_work: 0.4099 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3988 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 6379 Z= 0.166 Angle : 0.567 6.704 8699 Z= 0.289 Chirality : 0.042 0.297 969 Planarity : 0.004 0.044 1052 Dihedral : 8.861 58.420 1089 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 5.43 % Allowed : 28.42 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.40 (0.31), residues: 761 helix: 0.52 (0.26), residues: 387 sheet: -0.22 (0.53), residues: 102 loop : -1.35 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 66 HIS 0.001 0.000 HIS A 272 PHE 0.020 0.002 PHE A 585 TYR 0.017 0.002 TYR A 387 ARG 0.003 0.000 ARG A 181 Details of bonding type rmsd link_NAG-ASN : bond 0.00223 ( 1) link_NAG-ASN : angle 2.38694 ( 3) link_BETA1-4 : bond 0.00257 ( 1) link_BETA1-4 : angle 0.61745 ( 3) hydrogen bonds : bond 0.04594 ( 344) hydrogen bonds : angle 4.85645 ( 1005) SS BOND : bond 0.00538 ( 3) SS BOND : angle 0.95750 ( 6) covalent geometry : bond 0.00384 ( 6374) covalent geometry : angle 0.56475 ( 8687) *********************** 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 101 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 66 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: A 407 MET cc_start: 0.5963 (OUTLIER) cc_final: 0.5647 (mmm) REVERT: A 643 GLU cc_start: 0.6380 (OUTLIER) cc_final: 0.5344 (pm20) REVERT: B 47 ARG cc_start: 0.7363 (mtm180) cc_final: 0.7129 (mtp180) REVERT: B 74 ASP cc_start: 0.7937 (m-30) cc_final: 0.7627 (m-30) REVERT: B 97 THR cc_start: 0.7455 (OUTLIER) cc_final: 0.7183 (t) REVERT: C 129 GLU cc_start: 0.7281 (mt-10) cc_final: 0.7002 (mt-10) outliers start: 35 outliers final: 25 residues processed: 93 average time/residue: 0.7118 time to fit residues: 72.1825 Evaluate side-chains 93 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 65 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE 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 259 LEU 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 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 42 LYS 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 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 55 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 chunk 42 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 68 optimal weight: 0.0670 chunk 24 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 = 0.4430 r_free = 0.4430 target = 0.188983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.166110 restraints weight = 6586.574| |-----------------------------------------------------------------------------| r_work (start): 0.4232 rms_B_bonded: 1.75 r_work: 0.4155 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.4044 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.1683 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= 0.124 Angle : 0.516 5.874 8699 Z= 0.264 Chirality : 0.039 0.238 969 Planarity : 0.003 0.042 1052 Dihedral : 8.526 57.866 1089 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 5.28 % Allowed : 29.66 % Favored : 65.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.31), residues: 761 helix: 0.80 (0.26), residues: 378 sheet: -0.06 (0.54), residues: 102 loop : -1.15 (0.40), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 66 HIS 0.001 0.000 HIS A 180 PHE 0.014 0.001 PHE A 585 TYR 0.013 0.001 TYR A 395 ARG 0.005 0.000 ARG A 181 Details of bonding type rmsd link_NAG-ASN : bond 0.00539 ( 1) link_NAG-ASN : angle 2.23075 ( 3) link_BETA1-4 : bond 0.00412 ( 1) link_BETA1-4 : angle 0.72042 ( 3) hydrogen bonds : bond 0.04110 ( 344) hydrogen bonds : angle 4.70974 ( 1005) SS BOND : bond 0.00347 ( 3) SS BOND : angle 0.62270 ( 6) covalent geometry : bond 0.00276 ( 6374) covalent geometry : angle 0.51436 ( 8687) *********************** 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 103 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 69 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: A 414 PHE cc_start: 0.5677 (OUTLIER) cc_final: 0.5368 (m-10) REVERT: A 643 GLU cc_start: 0.6349 (OUTLIER) cc_final: 0.5216 (pm20) REVERT: B 47 ARG cc_start: 0.7383 (mtm180) cc_final: 0.7155 (mtp180) REVERT: B 74 ASP cc_start: 0.7961 (m-30) cc_final: 0.7680 (m-30) REVERT: B 97 THR cc_start: 0.7402 (OUTLIER) cc_final: 0.7115 (t) REVERT: C 129 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7113 (mt-10) outliers start: 34 outliers final: 22 residues processed: 97 average time/residue: 0.6879 time to fit residues: 72.7125 Evaluate side-chains 91 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 MET 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 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 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 458 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 42 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 60 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 55 optimal weight: 0.4980 chunk 14 optimal weight: 0.0050 chunk 50 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 40 optimal weight: 0.0870 chunk 34 optimal weight: 0.0270 chunk 69 optimal weight: 2.9990 overall best weight: 0.2630 ------------------------------------------------------------------------------- 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 = 0.4460 r_free = 0.4460 target = 0.192473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.171463 restraints weight = 6428.807| |-----------------------------------------------------------------------------| r_work (start): 0.4274 rms_B_bonded: 1.58 r_work: 0.4211 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.4112 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6379 Z= 0.109 Angle : 0.508 6.827 8699 Z= 0.259 Chirality : 0.039 0.219 969 Planarity : 0.003 0.039 1052 Dihedral : 8.144 58.518 1089 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.97 % Allowed : 28.42 % 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 (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: 0.05 (0.31), residues: 761 helix: 0.85 (0.26), residues: 381 sheet: 0.06 (0.54), residues: 102 loop : -1.06 (0.40), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 66 HIS 0.002 0.000 HIS A 180 PHE 0.017 0.001 PHE A 477 TYR 0.013 0.001 TYR A 395 ARG 0.004 0.000 ARG A 181 Details of bonding type rmsd link_NAG-ASN : bond 0.00588 ( 1) link_NAG-ASN : angle 2.27302 ( 3) link_BETA1-4 : bond 0.00555 ( 1) link_BETA1-4 : angle 0.87699 ( 3) hydrogen bonds : bond 0.03850 ( 344) hydrogen bonds : angle 4.59683 ( 1005) SS BOND : bond 0.00618 ( 3) SS BOND : angle 0.73952 ( 6) covalent geometry : bond 0.00235 ( 6374) covalent geometry : angle 0.50571 ( 8687) *********************** 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 102 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 70 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: A 414 PHE cc_start: 0.5648 (OUTLIER) cc_final: 0.5367 (m-10) REVERT: A 585 PHE cc_start: 0.6208 (OUTLIER) cc_final: 0.5987 (p90) REVERT: A 643 GLU cc_start: 0.6142 (OUTLIER) cc_final: 0.4985 (pm20) REVERT: B 42 LYS cc_start: 0.6874 (OUTLIER) cc_final: 0.6505 (tttt) REVERT: B 74 ASP cc_start: 0.7927 (m-30) cc_final: 0.7677 (m-30) REVERT: C 129 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7206 (mt-10) outliers start: 32 outliers final: 23 residues processed: 95 average time/residue: 0.6999 time to fit residues: 72.4344 Evaluate side-chains 93 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 MET 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 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 419 VAL Chi-restraints excluded: chain A residue 431 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 594 LEU 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 54 ASN Chi-restraints excluded: chain C residue 54 ILE 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 19 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 52 optimal weight: 0.0970 chunk 29 optimal weight: 0.4980 chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.4437 r_free = 0.4437 target = 0.189751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.166900 restraints weight = 6583.199| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 1.74 r_work: 0.4178 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.4071 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6379 Z= 0.134 Angle : 0.531 6.116 8699 Z= 0.271 Chirality : 0.040 0.268 969 Planarity : 0.003 0.040 1052 Dihedral : 7.981 59.955 1089 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 5.12 % Allowed : 29.04 % Favored : 65.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.21 (0.31), residues: 761 helix: 0.65 (0.26), residues: 389 sheet: 0.03 (0.54), residues: 102 loop : -1.28 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 66 HIS 0.001 0.000 HIS A 277 PHE 0.021 0.001 PHE A 477 TYR 0.017 0.001 TYR A 387 ARG 0.003 0.000 ARG A 181 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 1) link_NAG-ASN : angle 2.39036 ( 3) link_BETA1-4 : bond 0.00354 ( 1) link_BETA1-4 : angle 0.71272 ( 3) hydrogen bonds : bond 0.04162 ( 344) hydrogen bonds : angle 4.66241 ( 1005) SS BOND : bond 0.00406 ( 3) SS BOND : angle 1.08381 ( 6) covalent geometry : bond 0.00304 ( 6374) covalent geometry : angle 0.52871 ( 8687) *********************** 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 102 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 69 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 414 PHE cc_start: 0.5773 (OUTLIER) cc_final: 0.5426 (m-10) REVERT: A 643 GLU cc_start: 0.6212 (OUTLIER) cc_final: 0.5041 (pm20) REVERT: B 74 ASP cc_start: 0.7905 (m-30) cc_final: 0.7676 (m-30) REVERT: C 129 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7183 (mt-10) outliers start: 33 outliers final: 26 residues processed: 94 average time/residue: 0.6699 time to fit residues: 68.8832 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 : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 MET 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 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 640 THR Chi-restraints excluded: chain A residue 643 GLU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 88 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 36 optimal weight: 0.7980 chunk 16 optimal weight: 0.1980 chunk 39 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.187595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.164866 restraints weight = 6533.625| |-----------------------------------------------------------------------------| r_work (start): 0.4223 rms_B_bonded: 1.72 r_work: 0.4154 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.4046 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6379 Z= 0.137 Angle : 0.541 6.108 8699 Z= 0.275 Chirality : 0.040 0.261 969 Planarity : 0.003 0.040 1052 Dihedral : 7.761 59.586 1087 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 5.75 % Allowed : 28.57 % 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 (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: -0.29 (0.31), residues: 761 helix: 0.58 (0.26), residues: 388 sheet: 0.04 (0.55), residues: 102 loop : -1.33 (0.40), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 234 HIS 0.002 0.001 HIS A 260 PHE 0.018 0.001 PHE A 477 TYR 0.017 0.001 TYR A 387 ARG 0.002 0.000 ARG A 181 Details of bonding type rmsd link_NAG-ASN : bond 0.00435 ( 1) link_NAG-ASN : angle 2.39219 ( 3) link_BETA1-4 : bond 0.00429 ( 1) link_BETA1-4 : angle 0.73558 ( 3) hydrogen bonds : bond 0.04218 ( 344) hydrogen bonds : angle 4.67687 ( 1005) SS BOND : bond 0.00410 ( 3) SS BOND : angle 0.97676 ( 6) covalent geometry : bond 0.00312 ( 6374) covalent geometry : angle 0.53829 ( 8687) *********************** 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 103 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 66 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 414 PHE cc_start: 0.5808 (OUTLIER) cc_final: 0.5459 (m-10) REVERT: A 585 PHE cc_start: 0.6356 (OUTLIER) cc_final: 0.6117 (p90) REVERT: A 643 GLU cc_start: 0.6167 (OUTLIER) cc_final: 0.4917 (pm20) REVERT: B 74 ASP cc_start: 0.7912 (m-30) cc_final: 0.7680 (m-30) REVERT: C 129 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7184 (mt-10) outliers start: 37 outliers final: 26 residues processed: 94 average time/residue: 0.7149 time to fit residues: 73.3163 Evaluate side-chains 95 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 MET 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 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 42 LYS Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 80 SER 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 26 optimal weight: 0.1980 chunk 41 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 55 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4429 r_free = 0.4429 target = 0.189110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.166509 restraints weight = 6575.995| |-----------------------------------------------------------------------------| r_work (start): 0.4232 rms_B_bonded: 1.72 r_work: 0.4164 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.4060 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6379 Z= 0.126 Angle : 0.543 7.308 8699 Z= 0.273 Chirality : 0.040 0.271 969 Planarity : 0.003 0.039 1052 Dihedral : 7.625 59.541 1087 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 5.12 % Allowed : 28.73 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.21 (0.31), residues: 761 helix: 0.65 (0.26), residues: 388 sheet: 0.07 (0.54), residues: 102 loop : -1.29 (0.40), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 234 HIS 0.001 0.000 HIS A 180 PHE 0.018 0.001 PHE A 477 TYR 0.016 0.001 TYR A 387 ARG 0.003 0.000 ARG A 181 Details of bonding type rmsd link_NAG-ASN : bond 0.00448 ( 1) link_NAG-ASN : angle 2.38970 ( 3) link_BETA1-4 : bond 0.00387 ( 1) link_BETA1-4 : angle 0.79305 ( 3) hydrogen bonds : bond 0.04081 ( 344) hydrogen bonds : angle 4.62367 ( 1005) SS BOND : bond 0.00349 ( 3) SS BOND : angle 0.89234 ( 6) covalent geometry : bond 0.00282 ( 6374) covalent geometry : angle 0.54099 ( 8687) *********************** 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 102 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 69 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 414 PHE cc_start: 0.5839 (OUTLIER) cc_final: 0.5484 (m-10) REVERT: A 585 PHE cc_start: 0.6434 (OUTLIER) cc_final: 0.6195 (p90) REVERT: A 643 GLU cc_start: 0.6121 (OUTLIER) cc_final: 0.4861 (pm20) REVERT: B 42 LYS cc_start: 0.7037 (OUTLIER) cc_final: 0.6653 (tttt) REVERT: B 74 ASP cc_start: 0.7877 (m-30) cc_final: 0.7670 (m-30) outliers start: 33 outliers final: 26 residues processed: 95 average time/residue: 0.6865 time to fit residues: 71.1182 Evaluate side-chains 97 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 67 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 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 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 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 88 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 80 SER 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 12 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.188063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.166821 restraints weight = 6636.252| |-----------------------------------------------------------------------------| r_work (start): 0.4232 rms_B_bonded: 1.62 r_work: 0.4169 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.4066 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6379 Z= 0.144 Angle : 0.563 7.177 8699 Z= 0.284 Chirality : 0.041 0.268 969 Planarity : 0.003 0.040 1052 Dihedral : 7.614 58.591 1087 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 4.66 % Allowed : 29.35 % 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 (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: -0.30 (0.31), residues: 761 helix: 0.56 (0.26), residues: 387 sheet: 0.04 (0.55), residues: 102 loop : -1.33 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 234 HIS 0.001 0.000 HIS A 277 PHE 0.025 0.002 PHE A 477 TYR 0.018 0.001 TYR A 387 ARG 0.002 0.000 ARG A 181 Details of bonding type rmsd link_NAG-ASN : bond 0.00335 ( 1) link_NAG-ASN : angle 2.46009 ( 3) link_BETA1-4 : bond 0.00406 ( 1) link_BETA1-4 : angle 0.73810 ( 3) hydrogen bonds : bond 0.04275 ( 344) hydrogen bonds : angle 4.69524 ( 1005) SS BOND : bond 0.00444 ( 3) SS BOND : angle 1.04778 ( 6) covalent geometry : bond 0.00329 ( 6374) covalent geometry : angle 0.56021 ( 8687) ********************** 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 97 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 67 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: A 258 MET cc_start: 0.5399 (mpp) cc_final: 0.2573 (ttp) REVERT: A 414 PHE cc_start: 0.5865 (OUTLIER) cc_final: 0.5435 (m-10) REVERT: A 585 PHE cc_start: 0.6417 (OUTLIER) cc_final: 0.6141 (p90) REVERT: A 643 GLU cc_start: 0.6147 (OUTLIER) cc_final: 0.4838 (pm20) REVERT: B 74 ASP cc_start: 0.7888 (m-30) cc_final: 0.7688 (m-30) REVERT: B 127 MET cc_start: 0.6958 (mtt) cc_final: 0.6713 (mtt) outliers start: 30 outliers final: 26 residues processed: 91 average time/residue: 0.6795 time to fit residues: 67.5697 Evaluate side-chains 96 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 67 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 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 458 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 37 VAL Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 80 SER 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 54 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 42 optimal weight: 9.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.185729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.162926 restraints weight = 6733.696| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 1.74 r_work: 0.4139 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.4034 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6379 Z= 0.156 Angle : 0.586 7.123 8699 Z= 0.296 Chirality : 0.042 0.289 969 Planarity : 0.004 0.042 1052 Dihedral : 7.703 58.797 1087 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 4.81 % Allowed : 29.35 % Favored : 65.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.32 (0.31), residues: 761 helix: 0.52 (0.26), residues: 381 sheet: -0.02 (0.54), residues: 102 loop : -1.23 (0.40), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 234 HIS 0.001 0.000 HIS A 277 PHE 0.024 0.002 PHE A 477 TYR 0.019 0.002 TYR A 387 ARG 0.003 0.000 ARG A 644 Details of bonding type rmsd link_NAG-ASN : bond 0.00362 ( 1) link_NAG-ASN : angle 2.62470 ( 3) link_BETA1-4 : bond 0.00391 ( 1) link_BETA1-4 : angle 0.70139 ( 3) hydrogen bonds : bond 0.04482 ( 344) hydrogen bonds : angle 4.79567 ( 1005) SS BOND : bond 0.00473 ( 3) SS BOND : angle 1.14127 ( 6) covalent geometry : bond 0.00358 ( 6374) covalent geometry : angle 0.58361 ( 8687) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4947.02 seconds wall clock time: 85 minutes 18.29 seconds (5118.29 seconds total)