Starting phenix.real_space_refine on Fri Jan 17 10:07:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xk4_38415/01_2025/8xk4_38415.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xk4_38415/01_2025/8xk4_38415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xk4_38415/01_2025/8xk4_38415.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xk4_38415/01_2025/8xk4_38415.map" model { file = "/net/cci-nas-00/data/ceres_data/8xk4_38415/01_2025/8xk4_38415.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xk4_38415/01_2025/8xk4_38415.cif" } resolution = 2.94 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= 0.081 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5734 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 3 7.51 5 P 22 5.49 5 S 29 5.16 5 C 3791 2.51 5 N 1075 2.21 5 O 1128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 6048 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5589 Classifications: {'peptide': 689} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 23, 'TRANS': 665} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 255 Classifications: {'DNA': 12} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 11} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 179 Classifications: {'DNA': 9} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {' MN': 1} Classifications: {'DNA': 1, 'undetermined': 1} Modifications used: {'p5*END': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.21, per 1000 atoms: 0.70 Number of scatterers: 6048 At special positions: 0 Unit cell: (75.739, 89.355, 110.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 3 24.99 S 29 16.00 P 22 15.00 O 1128 8.00 N 1075 7.00 C 3791 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 757.6 milliseconds 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1312 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 9 sheets defined 33.4% alpha, 19.9% beta 8 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 36 through 48 Processing helix chain 'A' and resid 85 through 105 removed outlier: 3.538A pdb=" N ARG A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 165 removed outlier: 3.654A pdb=" N MET A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 288 removed outlier: 3.704A pdb=" N TRP A 282 " --> pdb=" O CYS A 278 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN A 285 " --> pdb=" O ARG A 281 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA A 288 " --> pdb=" O GLN A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 329 removed outlier: 4.200A pdb=" N GLY A 329 " --> pdb=" O VAL A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 354 Processing helix chain 'A' and resid 358 through 375 removed outlier: 3.583A pdb=" N ILE A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR A 363 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE A 365 " --> pdb=" O ASP A 361 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA A 375 " --> pdb=" O LYS A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.807A pdb=" N LYS A 387 " --> pdb=" O THR A 384 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER A 388 " --> pdb=" O SER A 385 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE A 389 " --> pdb=" O THR A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 389' Processing helix chain 'A' and resid 394 through 400 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 422 through 428 Processing helix chain 'A' and resid 432 through 442 removed outlier: 3.505A pdb=" N GLY A 442 " --> pdb=" O LYS A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 468 removed outlier: 3.666A pdb=" N ILE A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 488 Processing helix chain 'A' and resid 491 through 508 removed outlier: 4.115A pdb=" N THR A 495 " --> pdb=" O SER A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 585 Processing helix chain 'A' and resid 602 through 611 removed outlier: 3.552A pdb=" N VAL A 606 " --> pdb=" O HIS A 602 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU A 607 " --> pdb=" O THR A 603 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 614 No H-bonds generated for 'chain 'A' and resid 612 through 614' Processing helix chain 'A' and resid 681 through 693 removed outlier: 3.622A pdb=" N SER A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 721 removed outlier: 3.639A pdb=" N ARG A 721 " --> pdb=" O THR A 717 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 13 removed outlier: 5.151A pdb=" N ILE A 144 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL A 127 " --> pdb=" O GLN A 122 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLN A 122 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE A 129 " --> pdb=" O GLN A 120 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLN A 120 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLU A 131 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.785A pdb=" N VAL A 23 " --> pdb=" O GLU A 74 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLU A 74 " --> pdb=" O VAL A 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 187 Processing sheet with id=AA5, first strand: chain 'A' and resid 230 through 232 removed outlier: 4.065A pdb=" N ILE A 231 " --> pdb=" O TYR A 242 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N TYR A 242 " --> pdb=" O ILE A 231 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 308 through 311 removed outlier: 3.618A pdb=" N THR A 646 " --> pdb=" O CYS A 657 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N CYS A 522 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N HIS A 594 " --> pdb=" O CYS A 522 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE A 524 " --> pdb=" O HIS A 594 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ASP A 596 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ILE A 526 " --> pdb=" O ASP A 596 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AA8, first strand: chain 'A' and resid 378 through 382 removed outlier: 6.584A pdb=" N VAL A 417 " --> pdb=" O GLN A 450 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 528 through 531 removed outlier: 4.571A pdb=" N SER A 535 " --> pdb=" O LEU A 559 " (cutoff:3.500A) 220 hydrogen bonds defined for protein. 609 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 19 hydrogen bonds 38 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 2.07 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1617 1.33 - 1.45: 1195 1.45 - 1.57: 3312 1.57 - 1.69: 45 1.69 - 1.81: 51 Bond restraints: 6220 Sorted by residual: bond pdb=" P DC B 102 " pdb=" OP3 DC B 102 " ideal model delta sigma weight residual 1.480 1.606 -0.126 2.00e-02 2.50e+03 4.00e+01 bond pdb=" P DT C 7 " pdb=" OP3 DT C 7 " ideal model delta sigma weight residual 1.480 1.606 -0.126 2.00e-02 2.50e+03 3.94e+01 bond pdb=" P DT B 1 " pdb=" OP3 DT B 1 " ideal model delta sigma weight residual 1.480 1.600 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" N SER A 611 " pdb=" CA SER A 611 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.23e-02 6.61e+03 6.82e+00 bond pdb=" CA SER A 611 " pdb=" CB SER A 611 " ideal model delta sigma weight residual 1.528 1.490 0.039 1.59e-02 3.96e+03 5.89e+00 ... (remaining 6215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 8267 1.61 - 3.22: 188 3.22 - 4.83: 29 4.83 - 6.44: 11 6.44 - 8.05: 4 Bond angle restraints: 8499 Sorted by residual: angle pdb=" N PRO A 474 " pdb=" CA PRO A 474 " pdb=" CB PRO A 474 " ideal model delta sigma weight residual 103.25 111.30 -8.05 1.05e+00 9.07e-01 5.87e+01 angle pdb=" C PHE A 319 " pdb=" N HIS A 320 " pdb=" CA HIS A 320 " ideal model delta sigma weight residual 121.54 129.53 -7.99 1.91e+00 2.74e-01 1.75e+01 angle pdb=" N SER A 611 " pdb=" CA SER A 611 " pdb=" C SER A 611 " ideal model delta sigma weight residual 111.36 107.17 4.19 1.09e+00 8.42e-01 1.48e+01 angle pdb=" N ILE A 268 " pdb=" CA ILE A 268 " pdb=" C ILE A 268 " ideal model delta sigma weight residual 113.20 109.53 3.67 9.60e-01 1.09e+00 1.46e+01 angle pdb=" N VAL A 264 " pdb=" CA VAL A 264 " pdb=" C VAL A 264 " ideal model delta sigma weight residual 113.07 107.90 5.17 1.36e+00 5.41e-01 1.44e+01 ... (remaining 8494 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.68: 3463 27.68 - 55.35: 160 55.35 - 83.03: 13 83.03 - 110.71: 3 110.71 - 138.38: 1 Dihedral angle restraints: 3640 sinusoidal: 1612 harmonic: 2028 Sorted by residual: dihedral pdb=" CA LYS A 77 " pdb=" C LYS A 77 " pdb=" N ARG A 78 " pdb=" CA ARG A 78 " ideal model delta harmonic sigma weight residual -180.00 -156.88 -23.12 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA LEU A 270 " pdb=" C LEU A 270 " pdb=" N SER A 271 " pdb=" CA SER A 271 " ideal model delta harmonic sigma weight residual -180.00 -160.71 -19.29 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA ILE A 374 " pdb=" C ILE A 374 " pdb=" N ALA A 375 " pdb=" CA ALA A 375 " ideal model delta harmonic sigma weight residual 180.00 161.13 18.87 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 3637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 919 0.107 - 0.213: 25 0.213 - 0.320: 1 0.320 - 0.426: 0 0.426 - 0.533: 2 Chirality restraints: 947 Sorted by residual: chirality pdb=" P DT C 7 " pdb=" OP1 DT C 7 " pdb=" OP2 DT C 7 " pdb=" O5' DT C 7 " both_signs ideal model delta sigma weight residual True 2.35 2.88 -0.53 2.00e-01 2.50e+01 7.10e+00 chirality pdb=" P DC B 102 " pdb=" OP1 DC B 102 " pdb=" OP2 DC B 102 " pdb=" O5' DC B 102 " both_signs ideal model delta sigma weight residual True 2.35 -2.84 -0.50 2.00e-01 2.50e+01 6.18e+00 chirality pdb=" P DT B 1 " pdb=" OP1 DT B 1 " pdb=" OP2 DT B 1 " pdb=" O5' DT B 1 " both_signs ideal model delta sigma weight residual True 2.35 2.61 -0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 944 not shown) Planarity restraints: 1002 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 257 " 0.064 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO A 258 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT B 1 " 0.032 2.00e-02 2.50e+03 1.62e-02 6.60e+00 pdb=" N1 DT B 1 " -0.035 2.00e-02 2.50e+03 pdb=" C2 DT B 1 " 0.003 2.00e-02 2.50e+03 pdb=" O2 DT B 1 " -0.009 2.00e-02 2.50e+03 pdb=" N3 DT B 1 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DT B 1 " 0.007 2.00e-02 2.50e+03 pdb=" O4 DT B 1 " 0.014 2.00e-02 2.50e+03 pdb=" C5 DT B 1 " 0.002 2.00e-02 2.50e+03 pdb=" C7 DT B 1 " -0.009 2.00e-02 2.50e+03 pdb=" C6 DT B 1 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 510 " -0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO A 511 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 511 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 511 " -0.022 5.00e-02 4.00e+02 ... (remaining 999 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 18 2.38 - 3.01: 2986 3.01 - 3.64: 8479 3.64 - 4.27: 13700 4.27 - 4.90: 23035 Nonbonded interactions: 48218 Sorted by model distance: nonbonded pdb=" OP2 DT C 7 " pdb="MN MN C 101 " model vdw 1.749 2.320 nonbonded pdb=" O VAL A 737 " pdb="MN MN B 101 " model vdw 1.761 2.320 nonbonded pdb=" OP1 DT B 1 " pdb="MN MN B 101 " model vdw 1.807 2.320 nonbonded pdb=" OD1 ASP A 713 " pdb="MN MN C 101 " model vdw 1.941 2.320 nonbonded pdb=" OP1 DA B 3 " pdb="MN MN B 101 " model vdw 2.096 2.320 ... (remaining 48213 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.080 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 6220 Z= 0.259 Angle : 0.634 8.046 8499 Z= 0.370 Chirality : 0.050 0.533 947 Planarity : 0.005 0.095 1002 Dihedral : 15.225 138.384 2328 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.67 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.32), residues: 681 helix: -0.48 (0.37), residues: 203 sheet: 0.78 (0.45), residues: 146 loop : -1.52 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 43 HIS 0.007 0.001 HIS A 612 PHE 0.024 0.001 PHE A 319 TYR 0.018 0.001 TYR A 352 ARG 0.003 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.632 Fit side-chains REVERT: A 56 HIS cc_start: 0.7119 (m-70) cc_final: 0.6586 (m170) REVERT: A 310 ASP cc_start: 0.6192 (m-30) cc_final: 0.5751 (m-30) REVERT: A 539 MET cc_start: 0.7246 (mpp) cc_final: 0.6890 (mmt) REVERT: A 639 THR cc_start: 0.8538 (m) cc_final: 0.8309 (p) outliers start: 0 outliers final: 1 residues processed: 133 average time/residue: 1.1480 time to fit residues: 160.6273 Evaluate side-chains 88 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 17 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN A 183 GLN A 259 GLN A 461 GLN A 548 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.188925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.151326 restraints weight = 6108.436| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.71 r_work: 0.3453 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6220 Z= 0.199 Angle : 0.539 6.473 8499 Z= 0.299 Chirality : 0.043 0.169 947 Planarity : 0.004 0.054 1002 Dihedral : 12.887 139.674 978 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.99 % Allowed : 12.58 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.69 (0.32), residues: 681 helix: -0.10 (0.37), residues: 218 sheet: 1.04 (0.46), residues: 143 loop : -1.42 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 282 HIS 0.005 0.001 HIS A 590 PHE 0.023 0.001 PHE A 351 TYR 0.018 0.001 TYR A 37 ARG 0.007 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.645 Fit side-chains REVERT: A 56 HIS cc_start: 0.7719 (m-70) cc_final: 0.7224 (m170) REVERT: A 310 ASP cc_start: 0.6759 (m-30) cc_final: 0.6426 (m-30) REVERT: A 371 LYS cc_start: 0.8145 (tppt) cc_final: 0.7839 (mmmt) REVERT: A 539 MET cc_start: 0.8003 (mpp) cc_final: 0.7716 (mmt) outliers start: 12 outliers final: 3 residues processed: 107 average time/residue: 1.0361 time to fit residues: 117.3259 Evaluate side-chains 89 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 424 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 2 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 120 GLN A 548 HIS ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.181919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.147176 restraints weight = 6198.313| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.59 r_work: 0.3404 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6220 Z= 0.325 Angle : 0.611 7.193 8499 Z= 0.334 Chirality : 0.046 0.180 947 Planarity : 0.005 0.046 1002 Dihedral : 13.280 139.109 978 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.14 % Allowed : 14.24 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.93 (0.32), residues: 681 helix: -0.28 (0.36), residues: 217 sheet: 1.02 (0.46), residues: 137 loop : -1.60 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 282 HIS 0.006 0.001 HIS A 320 PHE 0.022 0.002 PHE A 319 TYR 0.019 0.002 TYR A 37 ARG 0.006 0.001 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.640 Fit side-chains REVERT: A 274 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7979 (mmtm) REVERT: A 310 ASP cc_start: 0.6936 (m-30) cc_final: 0.6598 (m-30) REVERT: A 371 LYS cc_start: 0.8153 (tppt) cc_final: 0.7843 (mmmt) REVERT: A 432 ARG cc_start: 0.6481 (mtm-85) cc_final: 0.6200 (mtp85) REVERT: A 643 ARG cc_start: 0.7602 (ttm-80) cc_final: 0.7156 (mtt180) REVERT: A 719 TYR cc_start: 0.8257 (OUTLIER) cc_final: 0.7613 (t80) outliers start: 25 outliers final: 8 residues processed: 100 average time/residue: 0.9701 time to fit residues: 102.9684 Evaluate side-chains 90 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 602 HIS Chi-restraints excluded: chain A residue 719 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 3.9990 chunk 47 optimal weight: 0.0040 chunk 19 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 46 optimal weight: 0.1980 chunk 56 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 259 GLN A 289 GLN A 548 HIS ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.186207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.151833 restraints weight = 6275.281| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.82 r_work: 0.3478 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6220 Z= 0.165 Angle : 0.497 5.701 8499 Z= 0.275 Chirality : 0.041 0.146 947 Planarity : 0.004 0.040 1002 Dihedral : 12.892 136.659 976 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.98 % Allowed : 16.23 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.53 (0.33), residues: 681 helix: 0.01 (0.36), residues: 225 sheet: 1.22 (0.46), residues: 143 loop : -1.38 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 512 HIS 0.006 0.001 HIS A 320 PHE 0.026 0.001 PHE A 86 TYR 0.015 0.001 TYR A 37 ARG 0.004 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.622 Fit side-chains REVERT: A 274 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7480 (mppt) REVERT: A 310 ASP cc_start: 0.6608 (m-30) cc_final: 0.6282 (m-30) REVERT: A 371 LYS cc_start: 0.8138 (tppt) cc_final: 0.7900 (mmmt) REVERT: A 540 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7604 (tpp) REVERT: A 643 ARG cc_start: 0.7400 (ttm-80) cc_final: 0.7075 (mtm180) REVERT: A 678 LYS cc_start: 0.8080 (pmmt) cc_final: 0.7491 (tppt) REVERT: A 689 VAL cc_start: 0.8027 (OUTLIER) cc_final: 0.7815 (p) outliers start: 18 outliers final: 3 residues processed: 101 average time/residue: 1.0172 time to fit residues: 108.6621 Evaluate side-chains 82 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 689 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 63 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 42 optimal weight: 20.0000 chunk 27 optimal weight: 0.3980 chunk 68 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 289 GLN A 548 HIS ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.177148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.139392 restraints weight = 6272.252| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.84 r_work: 0.3339 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6220 Z= 0.287 Angle : 0.586 7.184 8499 Z= 0.319 Chirality : 0.044 0.146 947 Planarity : 0.004 0.045 1002 Dihedral : 13.188 138.811 976 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.98 % Allowed : 17.72 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.78 (0.32), residues: 681 helix: -0.12 (0.35), residues: 222 sheet: 1.10 (0.46), residues: 137 loop : -1.54 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 282 HIS 0.004 0.001 HIS A 710 PHE 0.022 0.002 PHE A 319 TYR 0.014 0.001 TYR A 37 ARG 0.006 0.000 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.636 Fit side-chains REVERT: A 274 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7500 (mppt) REVERT: A 310 ASP cc_start: 0.7086 (m-30) cc_final: 0.6753 (m-30) REVERT: A 371 LYS cc_start: 0.8129 (tppt) cc_final: 0.7884 (mmmt) REVERT: A 608 LYS cc_start: 0.7908 (tppp) cc_final: 0.7650 (ttpt) REVERT: A 643 ARG cc_start: 0.7680 (ttm-80) cc_final: 0.7245 (mtt180) REVERT: A 678 LYS cc_start: 0.8135 (pmmt) cc_final: 0.7443 (tppt) REVERT: A 719 TYR cc_start: 0.8301 (OUTLIER) cc_final: 0.7754 (t80) outliers start: 18 outliers final: 7 residues processed: 94 average time/residue: 0.9471 time to fit residues: 94.8642 Evaluate side-chains 83 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 719 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 59 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN A 548 HIS ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.178666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.140688 restraints weight = 6177.745| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.89 r_work: 0.3342 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 6220 Z= 0.358 Angle : 0.630 6.936 8499 Z= 0.342 Chirality : 0.046 0.145 947 Planarity : 0.004 0.049 1002 Dihedral : 13.414 140.244 976 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.64 % Allowed : 18.21 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.31), residues: 681 helix: -0.40 (0.35), residues: 221 sheet: 1.01 (0.45), residues: 137 loop : -1.64 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 512 HIS 0.005 0.001 HIS A 710 PHE 0.032 0.002 PHE A 319 TYR 0.013 0.002 TYR A 37 ARG 0.004 0.001 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.656 Fit side-chains REVERT: A 133 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8292 (tt) REVERT: A 274 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7568 (mppt) REVERT: A 310 ASP cc_start: 0.7106 (m-30) cc_final: 0.6781 (m-30) REVERT: A 371 LYS cc_start: 0.8151 (tppt) cc_final: 0.7914 (mmmt) REVERT: A 608 LYS cc_start: 0.7897 (tppp) cc_final: 0.7586 (ttpt) REVERT: A 643 ARG cc_start: 0.7755 (ttm-80) cc_final: 0.7344 (mtt180) REVERT: A 678 LYS cc_start: 0.8040 (pmmt) cc_final: 0.7417 (tppt) REVERT: A 719 TYR cc_start: 0.8423 (OUTLIER) cc_final: 0.7848 (t80) outliers start: 22 outliers final: 6 residues processed: 95 average time/residue: 0.8726 time to fit residues: 88.5072 Evaluate side-chains 83 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 719 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 44 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 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 149 HIS A 548 HIS ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.184445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.147631 restraints weight = 6170.187| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.65 r_work: 0.3417 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6220 Z= 0.174 Angle : 0.515 5.924 8499 Z= 0.283 Chirality : 0.042 0.147 947 Planarity : 0.004 0.044 1002 Dihedral : 13.010 138.209 976 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.81 % Allowed : 20.03 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.64 (0.32), residues: 681 helix: -0.01 (0.36), residues: 224 sheet: 1.12 (0.45), residues: 137 loop : -1.43 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 512 HIS 0.003 0.001 HIS A 710 PHE 0.017 0.001 PHE A 86 TYR 0.014 0.001 TYR A 37 ARG 0.006 0.000 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: A 274 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7364 (mppt) REVERT: A 310 ASP cc_start: 0.6926 (m-30) cc_final: 0.6565 (m-30) REVERT: A 371 LYS cc_start: 0.8020 (tppt) cc_final: 0.7803 (mmmt) REVERT: A 608 LYS cc_start: 0.7810 (tppp) cc_final: 0.7509 (ttpt) REVERT: A 643 ARG cc_start: 0.7658 (ttm-80) cc_final: 0.7236 (mtt180) REVERT: A 678 LYS cc_start: 0.8064 (pmmt) cc_final: 0.7410 (tppt) REVERT: A 689 VAL cc_start: 0.8104 (OUTLIER) cc_final: 0.7860 (p) REVERT: A 719 TYR cc_start: 0.8212 (OUTLIER) cc_final: 0.7564 (t80) outliers start: 17 outliers final: 5 residues processed: 97 average time/residue: 1.0097 time to fit residues: 103.8177 Evaluate side-chains 83 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 719 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 66 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 HIS ** A 575 GLN ** 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 = 0.4002 r_free = 0.4002 target = 0.179280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.142756 restraints weight = 6116.404| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.67 r_work: 0.3379 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6220 Z= 0.297 Angle : 0.589 6.229 8499 Z= 0.321 Chirality : 0.044 0.145 947 Planarity : 0.004 0.048 1002 Dihedral : 13.245 139.897 976 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.98 % Allowed : 20.20 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.32), residues: 681 helix: -0.10 (0.36), residues: 222 sheet: 0.98 (0.45), residues: 137 loop : -1.52 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 282 HIS 0.004 0.001 HIS A 710 PHE 0.026 0.002 PHE A 319 TYR 0.014 0.001 TYR A 37 ARG 0.004 0.000 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.577 Fit side-chains REVERT: A 274 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7515 (mppt) REVERT: A 310 ASP cc_start: 0.7031 (m-30) cc_final: 0.6673 (m-30) REVERT: A 371 LYS cc_start: 0.7998 (tppt) cc_final: 0.7746 (mmmt) REVERT: A 540 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7798 (tpp) REVERT: A 608 LYS cc_start: 0.7811 (tppp) cc_final: 0.7525 (ttpt) REVERT: A 643 ARG cc_start: 0.7699 (ttm-80) cc_final: 0.7299 (mtt180) REVERT: A 678 LYS cc_start: 0.8014 (pmmt) cc_final: 0.7365 (tppt) REVERT: A 719 TYR cc_start: 0.8312 (OUTLIER) cc_final: 0.7659 (t80) outliers start: 18 outliers final: 7 residues processed: 89 average time/residue: 0.9137 time to fit residues: 86.6900 Evaluate side-chains 81 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 719 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 28 optimal weight: 5.9990 chunk 67 optimal weight: 0.4980 chunk 47 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 HIS ** A 575 GLN ** 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 = 0.4032 r_free = 0.4032 target = 0.182234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.145793 restraints weight = 6178.280| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 1.72 r_work: 0.3408 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6220 Z= 0.186 Angle : 0.534 7.187 8499 Z= 0.291 Chirality : 0.042 0.147 947 Planarity : 0.004 0.046 1002 Dihedral : 12.989 138.408 976 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.65 % Allowed : 21.03 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.59 (0.32), residues: 681 helix: 0.07 (0.36), residues: 226 sheet: 1.06 (0.45), residues: 137 loop : -1.39 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 512 HIS 0.003 0.001 HIS A 710 PHE 0.016 0.001 PHE A 319 TYR 0.014 0.001 TYR A 37 ARG 0.007 0.000 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: A 274 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7448 (mppt) REVERT: A 289 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7587 (mm-40) REVERT: A 310 ASP cc_start: 0.6955 (m-30) cc_final: 0.6589 (m-30) REVERT: A 371 LYS cc_start: 0.7978 (tppt) cc_final: 0.7737 (mmmt) REVERT: A 608 LYS cc_start: 0.7786 (tppp) cc_final: 0.7517 (ttpt) REVERT: A 643 ARG cc_start: 0.7670 (ttm-80) cc_final: 0.7270 (mtt180) REVERT: A 678 LYS cc_start: 0.8065 (pmmt) cc_final: 0.7403 (tppt) REVERT: A 689 VAL cc_start: 0.8180 (OUTLIER) cc_final: 0.7963 (p) REVERT: A 719 TYR cc_start: 0.8205 (OUTLIER) cc_final: 0.7557 (t80) outliers start: 16 outliers final: 6 residues processed: 93 average time/residue: 0.9301 time to fit residues: 92.3166 Evaluate side-chains 89 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 719 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 33 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 0.0670 chunk 13 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 HIS ** A 575 GLN ** 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 = 0.3995 r_free = 0.3995 target = 0.179080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.144150 restraints weight = 6252.156| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.58 r_work: 0.3382 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6220 Z= 0.219 Angle : 0.555 6.873 8499 Z= 0.304 Chirality : 0.043 0.198 947 Planarity : 0.004 0.045 1002 Dihedral : 12.997 138.578 976 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.99 % Allowed : 21.69 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.54 (0.32), residues: 681 helix: 0.11 (0.36), residues: 222 sheet: 1.07 (0.45), residues: 143 loop : -1.38 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 512 HIS 0.004 0.001 HIS A 710 PHE 0.019 0.002 PHE A 319 TYR 0.014 0.001 TYR A 37 ARG 0.004 0.000 ARG A 432 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.628 Fit side-chains REVERT: A 274 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7429 (mppt) REVERT: A 289 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7543 (mm-40) REVERT: A 310 ASP cc_start: 0.6997 (m-30) cc_final: 0.6622 (m-30) REVERT: A 371 LYS cc_start: 0.7949 (tppt) cc_final: 0.7729 (mmmt) REVERT: A 608 LYS cc_start: 0.7775 (tppp) cc_final: 0.7502 (ttpt) REVERT: A 643 ARG cc_start: 0.7711 (ttm-80) cc_final: 0.7303 (mtt180) REVERT: A 678 LYS cc_start: 0.8034 (pmmt) cc_final: 0.7372 (tppt) REVERT: A 719 TYR cc_start: 0.8188 (OUTLIER) cc_final: 0.7546 (t80) outliers start: 12 outliers final: 7 residues processed: 86 average time/residue: 0.9560 time to fit residues: 87.6658 Evaluate side-chains 86 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 719 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 66 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 HIS ** A 575 GLN ** 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 = 0.4017 r_free = 0.4017 target = 0.180476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.142456 restraints weight = 6204.140| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.81 r_work: 0.3377 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 6220 Z= 0.356 Angle : 0.639 6.504 8499 Z= 0.347 Chirality : 0.046 0.245 947 Planarity : 0.004 0.051 1002 Dihedral : 13.324 140.768 976 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.82 % Allowed : 22.68 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.77 (0.32), residues: 681 helix: -0.15 (0.36), residues: 219 sheet: 1.03 (0.45), residues: 143 loop : -1.50 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 512 HIS 0.005 0.001 HIS A 710 PHE 0.034 0.002 PHE A 319 TYR 0.013 0.002 TYR A 37 ARG 0.006 0.001 ARG A 291 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4447.50 seconds wall clock time: 80 minutes 48.48 seconds (4848.48 seconds total)