Starting phenix.real_space_refine on Sat May 10 18:28:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8de4_27384/05_2025/8de4_27384.cif Found real_map, /net/cci-nas-00/data/ceres_data/8de4_27384/05_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_27384/05_2025/8de4_27384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8de4_27384/05_2025/8de4_27384.map" model { file = "/net/cci-nas-00/data/ceres_data/8de4_27384/05_2025/8de4_27384.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8de4_27384/05_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-5687/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: 4.47, per 1000 atoms: 0.72 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: 1.78 Conformation dependent library (CDL) restraints added in 885.4 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: 0.82 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: 1.79 Time building geometry restraints manager: 2.03 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: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.700 Find NCS groups from input model: 0.060 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:10.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.710 ------------------------------------------------------------------------------- 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 : 0.637 Fit side-chains outliers start: 28 outliers final: 26 residues processed: 92 average time/residue: 0.6885 time to fit residues: 68.9997 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 : 0.597 ------------------------------------------------------------------------------- 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 = 42)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.169003 restraints weight = 6389.852| |-----------------------------------------------------------------------------| 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: 3.93 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 0.90359 ( 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 : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.5774 (OUTLIER) cc_final: 0.5484 (mmm) REVERT: A 414 PHE cc_start: 0.5605 (OUTLIER) cc_final: 0.5387 (m-10) REVERT: A 518 LEU cc_start: 0.6093 (tp) cc_final: 0.5739 (mt) REVERT: A 643 GLU cc_start: 0.6420 (OUTLIER) cc_final: 0.5326 (pm20) REVERT: B 47 ARG cc_start: 0.7225 (mtm180) cc_final: 0.6964 (mtp180) outliers start: 37 outliers final: 19 residues processed: 93 average time/residue: 0.7032 time to fit residues: 71.1899 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 : 0.571 ------------------------------------------------------------------------------- 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: 0.4980 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 68 optimal weight: 0.0270 chunk 26 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 42 optimal weight: 8.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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 = 0.4436 r_free = 0.4436 target = 0.189571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.166818 restraints weight = 6559.613| |-----------------------------------------------------------------------------| r_work (start): 0.4251 rms_B_bonded: 1.74 r_work: 0.4175 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.4063 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.1358 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= 0.131 Angle : 0.518 5.960 8699 Z= 0.265 Chirality : 0.040 0.256 969 Planarity : 0.004 0.048 1052 Dihedral : 9.050 58.093 1092 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 5.43 % Allowed : 27.95 % 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: 0.01 (0.31), residues: 761 helix: 0.92 (0.26), residues: 380 sheet: -0.38 (0.52), residues: 104 loop : -1.03 (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 272 PHE 0.016 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 0.00369 ( 1) link_NAG-ASN : angle 2.19943 ( 3) link_BETA1-4 : bond 0.00281 ( 1) link_BETA1-4 : angle 0.67723 ( 3) hydrogen bonds : bond 0.04258 ( 344) hydrogen bonds : angle 4.76084 ( 1005) SS BOND : bond 0.00328 ( 3) SS BOND : angle 0.61351 ( 6) covalent geometry : bond 0.00291 ( 6374) covalent geometry : angle 0.51662 ( 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 99 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 64 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 217 MET cc_start: 0.6209 (mmm) cc_final: 0.5913 (mmm) REVERT: A 407 MET cc_start: 0.6052 (OUTLIER) cc_final: 0.5737 (mmm) REVERT: A 518 LEU cc_start: 0.6315 (tp) cc_final: 0.6008 (mt) REVERT: A 643 GLU cc_start: 0.6316 (OUTLIER) cc_final: 0.5332 (pm20) REVERT: B 74 ASP cc_start: 0.8060 (m-30) cc_final: 0.7759 (m-30) REVERT: B 97 THR cc_start: 0.7354 (OUTLIER) cc_final: 0.7040 (t) outliers start: 35 outliers final: 21 residues processed: 92 average time/residue: 0.7129 time to fit residues: 71.7928 Evaluate side-chains 87 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 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 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: 0.5980 chunk 5 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 13 optimal weight: 0.0980 chunk 26 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4398 r_free = 0.4398 target = 0.186940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.163418 restraints weight = 6602.510| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 1.74 r_work: 0.4108 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3998 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6379 Z= 0.137 Angle : 0.528 6.652 8699 Z= 0.269 Chirality : 0.040 0.259 969 Planarity : 0.004 0.042 1052 Dihedral : 8.723 57.915 1089 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 5.28 % Allowed : 28.57 % 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: -0.11 (0.31), residues: 761 helix: 0.75 (0.26), residues: 381 sheet: -0.14 (0.53), residues: 102 loop : -1.10 (0.40), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 66 HIS 0.001 0.000 HIS A 277 PHE 0.017 0.001 PHE A 585 TYR 0.015 0.001 TYR A 387 ARG 0.005 0.000 ARG A 181 Details of bonding type rmsd link_NAG-ASN : bond 0.00389 ( 1) link_NAG-ASN : angle 2.22579 ( 3) link_BETA1-4 : bond 0.00333 ( 1) link_BETA1-4 : angle 0.61460 ( 3) hydrogen bonds : bond 0.04250 ( 344) hydrogen bonds : angle 4.74687 ( 1005) SS BOND : bond 0.00425 ( 3) SS BOND : angle 0.76932 ( 6) covalent geometry : bond 0.00313 ( 6374) covalent geometry : angle 0.52580 ( 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 100 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 66 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 407 MET cc_start: 0.5877 (OUTLIER) cc_final: 0.5638 (mmp) REVERT: A 518 LEU cc_start: 0.6459 (tp) cc_final: 0.6253 (mt) REVERT: A 643 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.5345 (pm20) REVERT: B 47 ARG cc_start: 0.7317 (mtm180) cc_final: 0.7090 (mtp180) REVERT: B 74 ASP cc_start: 0.8003 (m-30) cc_final: 0.7706 (m-30) REVERT: B 97 THR cc_start: 0.7429 (OUTLIER) cc_final: 0.7164 (t) REVERT: C 129 GLU cc_start: 0.7321 (mt-10) cc_final: 0.7026 (mt-10) outliers start: 34 outliers final: 22 residues processed: 93 average time/residue: 0.6410 time to fit residues: 65.1716 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 : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 463 ILE 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 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: 0.8980 chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 68 optimal weight: 0.0570 chunk 24 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 = 0.4414 r_free = 0.4414 target = 0.187273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.164355 restraints weight = 6621.251| |-----------------------------------------------------------------------------| r_work (start): 0.4197 rms_B_bonded: 1.75 r_work: 0.4117 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.4003 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 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 : 0.003 0.031 6379 Z= 0.143 Angle : 0.535 6.239 8699 Z= 0.273 Chirality : 0.040 0.265 969 Planarity : 0.004 0.042 1052 Dihedral : 8.501 57.897 1089 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 5.90 % Allowed : 28.42 % 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: -0.27 (0.31), residues: 761 helix: 0.63 (0.26), residues: 388 sheet: -0.08 (0.54), residues: 102 loop : -1.32 (0.40), residues: 271 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 0.017 0.001 PHE A 585 TYR 0.015 0.001 TYR A 387 ARG 0.003 0.000 ARG A 181 Details of bonding type rmsd link_NAG-ASN : bond 0.00360 ( 1) link_NAG-ASN : angle 2.24086 ( 3) link_BETA1-4 : bond 0.00484 ( 1) link_BETA1-4 : angle 0.70253 ( 3) hydrogen bonds : bond 0.04314 ( 344) hydrogen bonds : angle 4.72494 ( 1005) SS BOND : bond 0.00417 ( 3) SS BOND : angle 0.74272 ( 6) covalent geometry : bond 0.00323 ( 6374) covalent geometry : angle 0.53294 ( 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 108 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 70 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: A 217 MET cc_start: 0.6081 (OUTLIER) cc_final: 0.5715 (mtm) REVERT: A 414 PHE cc_start: 0.5803 (OUTLIER) cc_final: 0.5512 (m-10) REVERT: A 643 GLU cc_start: 0.6330 (OUTLIER) cc_final: 0.5203 (pm20) REVERT: B 74 ASP cc_start: 0.7990 (m-30) cc_final: 0.7746 (m-30) REVERT: B 97 THR cc_start: 0.7464 (OUTLIER) cc_final: 0.7181 (t) REVERT: C 129 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7153 (mt-10) outliers start: 38 outliers final: 25 residues processed: 99 average time/residue: 0.6434 time to fit residues: 69.8489 Evaluate side-chains 98 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 69 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 217 MET 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 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 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: 3.9990 chunk 49 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 55 optimal weight: 0.3980 chunk 14 optimal weight: 0.0020 chunk 50 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 overall best weight: 0.5188 ------------------------------------------------------------------------------- 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 = 0.188161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.165110 restraints weight = 6551.167| |-----------------------------------------------------------------------------| r_work (start): 0.4220 rms_B_bonded: 1.74 r_work: 0.4142 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.4033 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 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 0.029 6379 Z= 0.131 Angle : 0.536 6.847 8699 Z= 0.273 Chirality : 0.040 0.247 969 Planarity : 0.003 0.040 1052 Dihedral : 8.264 57.908 1089 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 6.21 % Allowed : 27.80 % 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: -0.15 (0.31), residues: 761 helix: 0.70 (0.26), residues: 382 sheet: -0.01 (0.54), residues: 102 loop : -1.17 (0.40), residues: 277 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 0.015 0.001 PHE A 585 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 0.00413 ( 1) link_NAG-ASN : angle 2.23389 ( 3) link_BETA1-4 : bond 0.00375 ( 1) link_BETA1-4 : angle 0.71232 ( 3) hydrogen bonds : bond 0.04162 ( 344) hydrogen bonds : angle 4.70619 ( 1005) SS BOND : bond 0.00366 ( 3) SS BOND : angle 0.86741 ( 6) covalent geometry : bond 0.00293 ( 6374) covalent geometry : angle 0.53436 ( 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 108 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 68 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: A 217 MET cc_start: 0.6067 (OUTLIER) cc_final: 0.5674 (mtm) REVERT: A 414 PHE cc_start: 0.5782 (OUTLIER) cc_final: 0.5487 (m-10) REVERT: A 643 GLU cc_start: 0.6310 (OUTLIER) cc_final: 0.5140 (pm20) REVERT: B 42 LYS cc_start: 0.6996 (OUTLIER) cc_final: 0.6600 (tttt) REVERT: B 74 ASP cc_start: 0.7972 (m-30) cc_final: 0.7713 (m-30) REVERT: C 129 GLU cc_start: 0.7418 (mt-10) cc_final: 0.7157 (mt-10) outliers start: 40 outliers final: 25 residues processed: 99 average time/residue: 0.6399 time to fit residues: 69.2204 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 : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 MET 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 458 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 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 94 SER 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: 1.9990 chunk 40 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 18 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4406 r_free = 0.4406 target = 0.186646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.164245 restraints weight = 6619.129| |-----------------------------------------------------------------------------| r_work (start): 0.4197 rms_B_bonded: 1.69 r_work: 0.4129 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.4024 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6379 Z= 0.159 Angle : 0.577 6.672 8699 Z= 0.294 Chirality : 0.042 0.290 969 Planarity : 0.004 0.042 1052 Dihedral : 8.103 58.438 1087 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 5.90 % Allowed : 28.11 % 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: 0.54 (0.26), residues: 381 sheet: -0.01 (0.55), residues: 102 loop : -1.21 (0.40), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 66 HIS 0.002 0.001 HIS A 260 PHE 0.018 0.002 PHE A 585 TYR 0.019 0.001 TYR A 387 ARG 0.002 0.000 ARG A 644 Details of bonding type rmsd link_NAG-ASN : bond 0.00244 ( 1) link_NAG-ASN : angle 2.44795 ( 3) link_BETA1-4 : bond 0.00389 ( 1) link_BETA1-4 : angle 0.69284 ( 3) hydrogen bonds : bond 0.04527 ( 344) hydrogen bonds : angle 4.80653 ( 1005) SS BOND : bond 0.00501 ( 3) SS BOND : angle 1.26164 ( 6) covalent geometry : bond 0.00364 ( 6374) covalent geometry : angle 0.57477 ( 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 107 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 69 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: A 217 MET cc_start: 0.6323 (OUTLIER) cc_final: 0.6045 (mtm) REVERT: A 414 PHE cc_start: 0.5969 (OUTLIER) cc_final: 0.5620 (m-10) REVERT: A 585 PHE cc_start: 0.6361 (OUTLIER) cc_final: 0.6111 (p90) REVERT: A 643 GLU cc_start: 0.6158 (OUTLIER) cc_final: 0.4900 (pm20) REVERT: B 74 ASP cc_start: 0.7939 (m-30) cc_final: 0.7691 (m-30) REVERT: C 129 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7186 (mt-10) outliers start: 38 outliers final: 28 residues processed: 98 average time/residue: 0.6132 time to fit residues: 65.9402 Evaluate side-chains 99 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 67 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 217 MET 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 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 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 44 SER Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 94 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 36 optimal weight: 0.5980 chunk 16 optimal weight: 0.1980 chunk 39 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.185816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.163071 restraints weight = 6561.848| |-----------------------------------------------------------------------------| r_work (start): 0.4209 rms_B_bonded: 1.72 r_work: 0.4144 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.4039 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.2028 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= 0.146 Angle : 0.565 7.326 8699 Z= 0.286 Chirality : 0.041 0.263 969 Planarity : 0.004 0.041 1052 Dihedral : 7.918 58.798 1087 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 5.90 % Allowed : 28.73 % Favored : 65.37 % 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: -0.25 (0.31), residues: 761 helix: 0.59 (0.26), residues: 380 sheet: -0.17 (0.55), residues: 104 loop : -1.14 (0.40), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.001 0.000 HIS A 260 PHE 0.016 0.001 PHE A 585 TYR 0.016 0.001 TYR A 387 ARG 0.003 0.000 ARG A 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00382 ( 1) link_NAG-ASN : angle 2.38582 ( 3) link_BETA1-4 : bond 0.00503 ( 1) link_BETA1-4 : angle 0.74456 ( 3) hydrogen bonds : bond 0.04348 ( 344) hydrogen bonds : angle 4.77355 ( 1005) SS BOND : bond 0.00439 ( 3) SS BOND : angle 1.03028 ( 6) covalent geometry : bond 0.00332 ( 6374) covalent geometry : angle 0.56261 ( 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 105 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 67 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: A 217 MET cc_start: 0.6239 (OUTLIER) cc_final: 0.5907 (mtm) REVERT: A 414 PHE cc_start: 0.5887 (OUTLIER) cc_final: 0.5463 (m-10) REVERT: A 585 PHE cc_start: 0.6385 (OUTLIER) cc_final: 0.6106 (p90) REVERT: A 643 GLU cc_start: 0.6176 (OUTLIER) cc_final: 0.4943 (pm20) REVERT: B 74 ASP cc_start: 0.7940 (m-30) cc_final: 0.7710 (m-30) REVERT: B 132 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.7122 (pt0) REVERT: C 129 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7158 (mt-10) outliers start: 38 outliers final: 30 residues processed: 97 average time/residue: 0.6695 time to fit residues: 70.7455 Evaluate side-chains 102 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 67 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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 217 MET 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 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 44 SER Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 132 GLN 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: 2.9990 chunk 41 optimal weight: 0.4980 chunk 20 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 58 optimal weight: 0.0770 chunk 1 optimal weight: 0.5980 chunk 55 optimal weight: 0.2980 chunk 43 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.4138 ------------------------------------------------------------------------------- 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 = 0.4421 r_free = 0.4421 target = 0.188320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.165475 restraints weight = 6586.800| |-----------------------------------------------------------------------------| r_work (start): 0.4234 rms_B_bonded: 1.74 r_work: 0.4168 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.4062 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.1960 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= 0.121 Angle : 0.541 7.544 8699 Z= 0.273 Chirality : 0.039 0.232 969 Planarity : 0.003 0.039 1052 Dihedral : 7.676 58.870 1087 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 5.28 % Allowed : 28.57 % 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: -0.18 (0.31), residues: 761 helix: 0.65 (0.26), residues: 388 sheet: 0.08 (0.55), residues: 102 loop : -1.25 (0.40), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.001 0.000 HIS A 180 PHE 0.014 0.001 PHE A 585 TYR 0.015 0.001 TYR A 387 ARG 0.003 0.000 ARG A 181 Details of bonding type rmsd link_NAG-ASN : bond 0.00462 ( 1) link_NAG-ASN : angle 2.38430 ( 3) link_BETA1-4 : bond 0.00358 ( 1) link_BETA1-4 : angle 0.83476 ( 3) hydrogen bonds : bond 0.04034 ( 344) hydrogen bonds : angle 4.68209 ( 1005) SS BOND : bond 0.00316 ( 3) SS BOND : angle 0.85847 ( 6) covalent geometry : bond 0.00268 ( 6374) covalent geometry : angle 0.53858 ( 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: 34 poor density : 68 time to evaluate : 0.604 Fit side-chains revert: symmetry clash REVERT: A 258 MET cc_start: 0.5415 (mpp) cc_final: 0.2565 (ttp) REVERT: A 414 PHE cc_start: 0.5762 (OUTLIER) cc_final: 0.5405 (m-10) REVERT: A 585 PHE cc_start: 0.6321 (OUTLIER) cc_final: 0.6073 (p90) REVERT: A 643 GLU cc_start: 0.6124 (OUTLIER) cc_final: 0.4915 (pm20) REVERT: B 42 LYS cc_start: 0.7028 (OUTLIER) cc_final: 0.6635 (tttt) REVERT: B 74 ASP cc_start: 0.7901 (m-30) cc_final: 0.7687 (m-30) REVERT: B 132 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.7079 (pt0) outliers start: 34 outliers final: 25 residues processed: 96 average time/residue: 0.6441 time to fit residues: 67.7692 Evaluate side-chains 95 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 65 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 MET 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 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 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 94 SER Chi-restraints excluded: chain B residue 132 GLN 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: 0.0050 chunk 41 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.2980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4426 r_free = 0.4426 target = 0.188909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.167760 restraints weight = 6606.311| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 1.61 r_work: 0.4178 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.4075 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.2011 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= 0.130 Angle : 0.545 7.356 8699 Z= 0.276 Chirality : 0.040 0.250 969 Planarity : 0.003 0.039 1052 Dihedral : 7.615 59.105 1087 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % 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: -0.21 (0.31), residues: 761 helix: 0.62 (0.26), residues: 387 sheet: 0.08 (0.55), residues: 102 loop : -1.24 (0.40), residues: 272 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 0.015 0.001 PHE A 585 TYR 0.016 0.001 TYR A 387 ARG 0.002 0.000 ARG A 644 Details of bonding type rmsd link_NAG-ASN : bond 0.00396 ( 1) link_NAG-ASN : angle 2.42311 ( 3) link_BETA1-4 : bond 0.00406 ( 1) link_BETA1-4 : angle 0.80781 ( 3) hydrogen bonds : bond 0.04116 ( 344) hydrogen bonds : angle 4.70046 ( 1005) SS BOND : bond 0.00375 ( 3) SS BOND : angle 0.92817 ( 6) covalent geometry : bond 0.00291 ( 6374) covalent geometry : angle 0.54238 ( 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 98 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 67 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: A 258 MET cc_start: 0.5413 (mpp) cc_final: 0.2567 (ttp) REVERT: A 414 PHE cc_start: 0.5806 (OUTLIER) cc_final: 0.5448 (m-10) REVERT: A 585 PHE cc_start: 0.6387 (OUTLIER) cc_final: 0.6158 (p90) REVERT: A 643 GLU cc_start: 0.6032 (OUTLIER) cc_final: 0.5749 (pm20) REVERT: B 42 LYS cc_start: 0.7005 (OUTLIER) cc_final: 0.6635 (tttt) REVERT: B 132 GLN cc_start: 0.7543 (OUTLIER) cc_final: 0.7089 (pt0) outliers start: 31 outliers final: 24 residues processed: 92 average time/residue: 0.7211 time to fit residues: 72.0319 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 : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 MET 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 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 37 VAL Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 132 GLN 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: 0.5980 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 42 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4403 r_free = 0.4403 target = 0.186225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.163297 restraints weight = 6710.555| |-----------------------------------------------------------------------------| r_work (start): 0.4209 rms_B_bonded: 1.74 r_work: 0.4141 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.4034 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.2094 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= 0.147 Angle : 0.567 7.358 8699 Z= 0.287 Chirality : 0.041 0.273 969 Planarity : 0.003 0.041 1052 Dihedral : 7.647 59.754 1087 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 5.43 % Allowed : 28.73 % 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: -0.29 (0.31), residues: 761 helix: 0.54 (0.26), residues: 386 sheet: 0.03 (0.55), residues: 102 loop : -1.26 (0.40), residues: 273 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 0.016 0.001 PHE A 585 TYR 0.017 0.001 TYR A 387 ARG 0.002 0.000 ARG A 644 Details of bonding type rmsd link_NAG-ASN : bond 0.00315 ( 1) link_NAG-ASN : angle 2.49738 ( 3) link_BETA1-4 : bond 0.00433 ( 1) link_BETA1-4 : angle 0.73902 ( 3) hydrogen bonds : bond 0.04320 ( 344) hydrogen bonds : angle 4.75903 ( 1005) SS BOND : bond 0.00443 ( 3) SS BOND : angle 1.02854 ( 6) covalent geometry : bond 0.00335 ( 6374) covalent geometry : angle 0.56450 ( 8687) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4758.82 seconds wall clock time: 82 minutes 39.66 seconds (4959.66 seconds total)