Starting phenix.real_space_refine on Sat Oct 11 02:23:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xhv_38355/10_2025/8xhv_38355.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xhv_38355/10_2025/8xhv_38355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xhv_38355/10_2025/8xhv_38355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xhv_38355/10_2025/8xhv_38355.map" model { file = "/net/cci-nas-00/data/ceres_data/8xhv_38355/10_2025/8xhv_38355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xhv_38355/10_2025/8xhv_38355.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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 5813 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 1 7.51 5 P 14 5.49 5 S 29 5.16 5 C 3907 2.51 5 N 1092 2.21 5 O 1156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6199 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5879 Classifications: {'peptide': 721} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 23, 'TRANS': 697} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 295 Classifications: {'DNA': 14} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 13} Chain breaks: 1 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1, 'water': 19} Link IDs: {None: 19} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 1.56, per 1000 atoms: 0.25 Number of scatterers: 6199 At special positions: 0 Unit cell: (73.186, 92.759, 106.375, 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 1 24.99 S 29 16.00 P 14 15.00 O 1156 8.00 N 1092 7.00 C 3907 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: 0.40 Conformation dependent library (CDL) restraints added in 325.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1378 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 7 sheets defined 38.4% alpha, 19.6% beta 0 base pairs and 6 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 13 through 17 removed outlier: 3.854A pdb=" N LEU A 17 " --> pdb=" O ALA A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 48 Processing helix chain 'A' and resid 84 through 108 removed outlier: 3.664A pdb=" N HIS A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 166 Processing helix chain 'A' and resid 207 through 216 Processing helix chain 'A' and resid 257 through 268 Processing helix chain 'A' and resid 271 through 288 Processing helix chain 'A' and resid 301 through 306 Processing helix chain 'A' and resid 325 through 332 Processing helix chain 'A' and resid 349 through 356 Processing helix chain 'A' and resid 358 through 375 removed outlier: 3.922A pdb=" N ALA A 375 " --> pdb=" O LYS A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 400 removed outlier: 3.736A pdb=" N PHE A 398 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 394 through 400' Processing helix chain 'A' and resid 400 through 405 Processing helix chain 'A' and resid 406 through 409 removed outlier: 3.519A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 409' Processing helix chain 'A' and resid 422 through 428 Processing helix chain 'A' and resid 432 through 445 removed outlier: 3.797A pdb=" N GLY A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 467 Processing helix chain 'A' and resid 476 through 489 removed outlier: 3.845A pdb=" N CYS A 480 " --> pdb=" O ASP A 476 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASN A 489 " --> pdb=" O ASP A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 507 removed outlier: 4.133A 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 613 removed outlier: 4.147A pdb=" N VAL A 606 " --> pdb=" O HIS A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 692 Processing helix chain 'A' and resid 693 through 695 No H-bonds generated for 'chain 'A' and resid 693 through 695' Processing helix chain 'A' and resid 706 through 721 removed outlier: 3.912A pdb=" N ALA A 712 " --> pdb=" O THR A 708 " (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 9 removed outlier: 6.810A pdb=" N VAL A 127 " --> pdb=" O GLN A 122 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLN A 122 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ILE A 129 " --> pdb=" O GLN A 120 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N GLN A 120 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 4.481A 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 53 removed outlier: 3.926A pdb=" N GLU A 74 " --> pdb=" O VAL A 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 241 through 243 removed outlier: 4.116A pdb=" N VAL A 230 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASN A 191 " --> pdb=" O HIS A 232 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 311 removed outlier: 3.576A pdb=" N THR A 646 " --> pdb=" O CYS A 657 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE A 591 " --> pdb=" O ASP A 618 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL A 620 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE A 593 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ILE A 622 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ARG A 595 " --> pdb=" O ILE A 622 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE A 524 " --> pdb=" O HIS A 594 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ASP A 596 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ILE A 526 " --> pdb=" O ASP A 596 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N MET A 539 " --> pdb=" O ALA A 553 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AA7, first strand: chain 'A' and resid 378 through 382 removed outlier: 6.583A pdb=" N GLY A 339 " --> pdb=" O ASN A 379 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N THR A 381 " --> pdb=" O GLY A 339 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE A 341 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N THR A 416 " --> pdb=" O ASN A 340 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LYS A 342 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LEU A 418 " --> pdb=" O LYS A 342 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N SER A 344 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N PHE A 420 " --> pdb=" O SER A 344 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU A 346 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL A 417 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ILE A 452 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ALA A 419 " --> pdb=" O ILE A 452 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 248 hydrogen bonds defined for protein. 705 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 6 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1714 1.33 - 1.45: 1150 1.45 - 1.57: 3407 1.57 - 1.69: 27 1.69 - 1.81: 50 Bond restraints: 6348 Sorted by residual: 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 3.58e+01 bond pdb=" C1' DT B 1 " pdb=" N1 DT B 1 " ideal model delta sigma weight residual 1.490 1.459 0.031 3.00e-02 1.11e+03 1.10e+00 bond pdb=" C3' G B 11 " pdb=" C2' G B 11 " ideal model delta sigma weight residual 1.525 1.544 -0.019 2.00e-02 2.50e+03 8.99e-01 bond pdb=" O4' G B 11 " pdb=" C1' G B 11 " ideal model delta sigma weight residual 1.414 1.397 0.017 2.00e-02 2.50e+03 7.63e-01 bond pdb=" C4' A B 17 " pdb=" O4' A B 17 " ideal model delta sigma weight residual 1.450 1.434 0.016 2.00e-02 2.50e+03 6.26e-01 ... (remaining 6343 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 8480 1.73 - 3.46: 155 3.46 - 5.20: 13 5.20 - 6.93: 3 6.93 - 8.66: 3 Bond angle restraints: 8654 Sorted by residual: angle pdb=" OP2 DT B 1 " pdb=" P DT B 1 " pdb=" OP3 DT B 1 " ideal model delta sigma weight residual 109.47 118.13 -8.66 3.00e+00 1.11e-01 8.33e+00 angle pdb=" N ILE A 709 " pdb=" CA ILE A 709 " pdb=" C ILE A 709 " ideal model delta sigma weight residual 112.96 110.09 2.87 1.00e+00 1.00e+00 8.21e+00 angle pdb=" O5' DT B 1 " pdb=" P DT B 1 " pdb=" OP3 DT B 1 " ideal model delta sigma weight residual 109.47 101.27 8.20 3.00e+00 1.11e-01 7.47e+00 angle pdb=" C4 DT B 1 " pdb=" C5 DT B 1 " pdb=" C7 DT B 1 " ideal model delta sigma weight residual 122.40 118.89 3.51 1.50e+00 4.44e-01 5.49e+00 angle pdb=" OP1 DT B 1 " pdb=" P DT B 1 " pdb=" OP2 DT B 1 " ideal model delta sigma weight residual 120.00 113.16 6.84 3.00e+00 1.11e-01 5.20e+00 ... (remaining 8649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 3262 16.49 - 32.98: 356 32.98 - 49.47: 86 49.47 - 65.96: 30 65.96 - 82.44: 10 Dihedral angle restraints: 3744 sinusoidal: 1611 harmonic: 2133 Sorted by residual: dihedral pdb=" CA PHE A 319 " pdb=" C PHE A 319 " pdb=" N HIS A 320 " pdb=" CA HIS A 320 " ideal model delta harmonic sigma weight residual 180.00 157.66 22.34 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA GLY A 544 " pdb=" C GLY A 544 " pdb=" N SER A 545 " pdb=" CA SER A 545 " ideal model delta harmonic sigma weight residual 180.00 158.70 21.30 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA TYR A 242 " pdb=" C TYR A 242 " pdb=" N ALA A 243 " pdb=" CA ALA A 243 " ideal model delta harmonic sigma weight residual 180.00 -162.01 -17.99 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 3741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 884 0.080 - 0.159: 80 0.159 - 0.239: 0 0.239 - 0.319: 0 0.319 - 0.399: 1 Chirality restraints: 965 Sorted by residual: 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 -2.74 -0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" CA ILE A 671 " pdb=" N ILE A 671 " pdb=" C ILE A 671 " pdb=" CB ILE A 671 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CG LEU A 734 " pdb=" CB LEU A 734 " pdb=" CD1 LEU A 734 " pdb=" CD2 LEU A 734 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.60e-01 ... (remaining 962 not shown) Planarity restraints: 1047 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT B 1 " 0.020 2.00e-02 2.50e+03 9.11e-03 2.08e+00 pdb=" N1 DT B 1 " -0.015 2.00e-02 2.50e+03 pdb=" C2 DT B 1 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DT B 1 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DT B 1 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DT B 1 " 0.000 2.00e-02 2.50e+03 pdb=" O4 DT B 1 " 0.011 2.00e-02 2.50e+03 pdb=" C5 DT B 1 " -0.005 2.00e-02 2.50e+03 pdb=" C7 DT B 1 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DT B 1 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 510 " -0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO A 511 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 511 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 511 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 734 " -0.006 2.00e-02 2.50e+03 1.23e-02 1.51e+00 pdb=" C LEU A 734 " 0.021 2.00e-02 2.50e+03 pdb=" O LEU A 734 " -0.008 2.00e-02 2.50e+03 pdb=" N PRO A 735 " -0.007 2.00e-02 2.50e+03 ... (remaining 1044 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.35: 14 2.35 - 2.99: 2948 2.99 - 3.63: 8869 3.63 - 4.26: 14177 4.26 - 4.90: 24028 Nonbonded interactions: 50036 Sorted by model distance: nonbonded pdb=" O VAL A 737 " pdb="MN MN A 801 " model vdw 1.715 2.320 nonbonded pdb=" OP1 A B 3 " pdb="MN MN A 801 " model vdw 1.857 2.320 nonbonded pdb=" C VAL A 737 " pdb="MN MN A 801 " model vdw 1.982 2.550 nonbonded pdb=" OXT VAL A 737 " pdb="MN MN A 801 " model vdw 2.066 2.320 nonbonded pdb=" OH TYR A 37 " pdb=" NH2 ARG A 41 " model vdw 2.230 3.120 ... (remaining 50031 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.060 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 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 : 0.003 0.120 6348 Z= 0.148 Angle : 0.572 8.661 8654 Z= 0.309 Chirality : 0.044 0.399 965 Planarity : 0.003 0.032 1047 Dihedral : 15.522 82.445 2366 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.31), residues: 715 helix: 1.39 (0.33), residues: 248 sheet: 0.71 (0.46), residues: 123 loop : -1.39 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 105 TYR 0.019 0.001 TYR A 242 PHE 0.020 0.001 PHE A 351 TRP 0.009 0.001 TRP A 282 HIS 0.006 0.001 HIS A 602 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 6348) covalent geometry : angle 0.57249 ( 8654) hydrogen bonds : bond 0.12985 ( 248) hydrogen bonds : angle 6.64448 ( 705) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 159 THR cc_start: 0.7198 (p) cc_final: 0.6997 (t) REVERT: A 322 ASP cc_start: 0.7756 (m-30) cc_final: 0.7534 (m-30) REVERT: A 439 GLN cc_start: 0.7565 (pt0) cc_final: 0.7034 (mt0) REVERT: A 600 ARG cc_start: 0.7349 (ptp-110) cc_final: 0.7135 (ptp-170) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.5855 time to fit residues: 76.4077 Evaluate side-chains 85 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.0170 chunk 27 optimal weight: 2.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 541 ASN A 571 ASN A 663 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.189521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.143648 restraints weight = 6467.238| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.30 r_work: 0.3336 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6348 Z= 0.134 Angle : 0.543 6.418 8654 Z= 0.301 Chirality : 0.043 0.148 965 Planarity : 0.004 0.035 1047 Dihedral : 12.362 74.633 943 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.03 % Allowed : 11.41 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.31), residues: 715 helix: 1.48 (0.34), residues: 254 sheet: 0.61 (0.42), residues: 160 loop : -1.56 (0.32), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 291 TYR 0.018 0.001 TYR A 242 PHE 0.023 0.002 PHE A 401 TRP 0.013 0.001 TRP A 282 HIS 0.006 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 6348) covalent geometry : angle 0.54339 ( 8654) hydrogen bonds : bond 0.04319 ( 248) hydrogen bonds : angle 5.00912 ( 705) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.223 Fit side-chains REVERT: A 174 MET cc_start: 0.7002 (ttp) cc_final: 0.6440 (ptm) REVERT: A 183 GLN cc_start: 0.5828 (mm-40) cc_final: 0.5172 (mt0) REVERT: A 322 ASP cc_start: 0.7495 (m-30) cc_final: 0.7031 (m-30) REVERT: A 435 GLN cc_start: 0.6968 (pt0) cc_final: 0.6503 (mp10) REVERT: A 439 GLN cc_start: 0.7627 (pt0) cc_final: 0.6934 (mt0) REVERT: A 576 MET cc_start: 0.7709 (mmp) cc_final: 0.7508 (mmp) REVERT: A 600 ARG cc_start: 0.7994 (ptp-110) cc_final: 0.7780 (ptp-170) outliers start: 13 outliers final: 4 residues processed: 108 average time/residue: 0.5348 time to fit residues: 60.4918 Evaluate side-chains 82 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 573 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 17 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 548 HIS A 571 ASN A 638 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.186834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.131069 restraints weight = 6499.624| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.21 r_work: 0.3283 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6348 Z= 0.195 Angle : 0.607 9.246 8654 Z= 0.330 Chirality : 0.046 0.155 965 Planarity : 0.004 0.038 1047 Dihedral : 12.483 73.731 943 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.75 % Allowed : 13.75 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.31), residues: 715 helix: 1.18 (0.33), residues: 257 sheet: 0.58 (0.42), residues: 155 loop : -1.51 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 291 TYR 0.024 0.002 TYR A 242 PHE 0.018 0.002 PHE A 401 TRP 0.010 0.001 TRP A 282 HIS 0.005 0.001 HIS A 602 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 6348) covalent geometry : angle 0.60715 ( 8654) hydrogen bonds : bond 0.05188 ( 248) hydrogen bonds : angle 4.97544 ( 705) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.230 Fit side-chains REVERT: A 12 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.6986 (mp0) REVERT: A 38 HIS cc_start: 0.7096 (OUTLIER) cc_final: 0.6472 (p90) REVERT: A 159 THR cc_start: 0.7424 (m) cc_final: 0.7190 (m) REVERT: A 174 MET cc_start: 0.7033 (ttp) cc_final: 0.6402 (ptm) REVERT: A 183 GLN cc_start: 0.5897 (mm-40) cc_final: 0.5385 (mt0) REVERT: A 270 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8512 (mt) REVERT: A 414 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7475 (mp10) REVERT: A 435 GLN cc_start: 0.7205 (pt0) cc_final: 0.6830 (mp10) REVERT: A 600 ARG cc_start: 0.8027 (ptp-110) cc_final: 0.7791 (ptp-170) outliers start: 24 outliers final: 11 residues processed: 99 average time/residue: 0.5440 time to fit residues: 56.5479 Evaluate side-chains 93 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 662 GLN Chi-restraints excluded: chain A residue 663 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 54 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 364 GLN A 571 ASN A 638 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.186318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.140099 restraints weight = 6536.479| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.54 r_work: 0.3289 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6348 Z= 0.193 Angle : 0.608 10.591 8654 Z= 0.330 Chirality : 0.045 0.160 965 Planarity : 0.004 0.039 1047 Dihedral : 12.611 74.477 943 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.22 % Allowed : 16.09 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.31), residues: 715 helix: 1.02 (0.33), residues: 257 sheet: 0.52 (0.42), residues: 155 loop : -1.53 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 291 TYR 0.023 0.002 TYR A 242 PHE 0.019 0.002 PHE A 401 TRP 0.012 0.001 TRP A 282 HIS 0.005 0.001 HIS A 602 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 6348) covalent geometry : angle 0.60816 ( 8654) hydrogen bonds : bond 0.04908 ( 248) hydrogen bonds : angle 4.86681 ( 705) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 0.182 Fit side-chains REVERT: A 12 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7089 (mp0) REVERT: A 38 HIS cc_start: 0.7180 (OUTLIER) cc_final: 0.6473 (p90) REVERT: A 159 THR cc_start: 0.7438 (m) cc_final: 0.7234 (m) REVERT: A 183 GLN cc_start: 0.5951 (mm-40) cc_final: 0.5492 (mt0) REVERT: A 270 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8534 (mt) REVERT: A 322 ASP cc_start: 0.7738 (m-30) cc_final: 0.7395 (m-30) REVERT: A 414 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7473 (mp10) REVERT: A 435 GLN cc_start: 0.7313 (pt0) cc_final: 0.6880 (mp10) REVERT: A 509 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7563 (mt) REVERT: A 600 ARG cc_start: 0.8039 (ptp-110) cc_final: 0.7781 (ptp-170) outliers start: 27 outliers final: 13 residues processed: 100 average time/residue: 0.4701 time to fit residues: 49.3706 Evaluate side-chains 99 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 662 GLN Chi-restraints excluded: chain A residue 663 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 31 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 52 optimal weight: 20.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 571 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.186289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.130338 restraints weight = 6652.947| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.21 r_work: 0.3274 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6348 Z= 0.184 Angle : 0.600 11.252 8654 Z= 0.325 Chirality : 0.045 0.154 965 Planarity : 0.004 0.039 1047 Dihedral : 12.591 74.332 943 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 4.06 % Allowed : 18.12 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.31), residues: 715 helix: 0.95 (0.33), residues: 257 sheet: 0.47 (0.42), residues: 155 loop : -1.55 (0.32), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 13 TYR 0.023 0.002 TYR A 242 PHE 0.018 0.002 PHE A 401 TRP 0.012 0.001 TRP A 282 HIS 0.003 0.001 HIS A 602 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 6348) covalent geometry : angle 0.60034 ( 8654) hydrogen bonds : bond 0.04828 ( 248) hydrogen bonds : angle 4.80246 ( 705) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.166 Fit side-chains REVERT: A 12 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7295 (mp0) REVERT: A 38 HIS cc_start: 0.7191 (OUTLIER) cc_final: 0.6521 (p90) REVERT: A 159 THR cc_start: 0.7415 (m) cc_final: 0.7203 (m) REVERT: A 183 GLN cc_start: 0.5967 (mm-40) cc_final: 0.5522 (mt0) REVERT: A 270 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8524 (mt) REVERT: A 322 ASP cc_start: 0.7726 (m-30) cc_final: 0.7394 (m-30) REVERT: A 435 GLN cc_start: 0.7331 (pt0) cc_final: 0.6853 (mp10) REVERT: A 509 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7560 (mt) REVERT: A 600 ARG cc_start: 0.8078 (ptp-110) cc_final: 0.7822 (ptp-170) REVERT: A 734 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.6913 (tt) outliers start: 26 outliers final: 16 residues processed: 99 average time/residue: 0.5147 time to fit residues: 53.5473 Evaluate side-chains 99 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 662 GLN Chi-restraints excluded: chain A residue 734 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 59 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 48 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 571 ASN A 638 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.188066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.132807 restraints weight = 6563.956| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.19 r_work: 0.3290 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6348 Z= 0.140 Angle : 0.559 11.736 8654 Z= 0.302 Chirality : 0.043 0.148 965 Planarity : 0.003 0.037 1047 Dihedral : 12.514 75.485 943 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 4.06 % Allowed : 18.91 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.31), residues: 715 helix: 1.05 (0.33), residues: 257 sheet: 0.52 (0.42), residues: 155 loop : -1.58 (0.32), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 291 TYR 0.018 0.001 TYR A 242 PHE 0.011 0.001 PHE A 86 TRP 0.013 0.001 TRP A 282 HIS 0.003 0.001 HIS A 696 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 6348) covalent geometry : angle 0.55945 ( 8654) hydrogen bonds : bond 0.04105 ( 248) hydrogen bonds : angle 4.65605 ( 705) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.199 Fit side-chains REVERT: A 12 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7213 (mp0) REVERT: A 38 HIS cc_start: 0.7126 (OUTLIER) cc_final: 0.6397 (p90) REVERT: A 183 GLN cc_start: 0.5950 (mm-40) cc_final: 0.5475 (mt0) REVERT: A 270 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8463 (mt) REVERT: A 322 ASP cc_start: 0.7595 (m-30) cc_final: 0.7237 (m-30) REVERT: A 414 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7514 (mp10) REVERT: A 435 GLN cc_start: 0.7377 (pt0) cc_final: 0.6909 (mp10) REVERT: A 600 ARG cc_start: 0.8047 (ptp-110) cc_final: 0.7788 (ptp-170) REVERT: A 734 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.6984 (tt) outliers start: 26 outliers final: 14 residues processed: 102 average time/residue: 0.4917 time to fit residues: 52.7903 Evaluate side-chains 98 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 663 GLN Chi-restraints excluded: chain A residue 734 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 571 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.187564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.131759 restraints weight = 6573.966| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.18 r_work: 0.3288 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6348 Z= 0.151 Angle : 0.573 11.852 8654 Z= 0.309 Chirality : 0.043 0.154 965 Planarity : 0.003 0.037 1047 Dihedral : 12.531 75.516 943 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 4.69 % Allowed : 19.22 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.30), residues: 715 helix: 1.19 (0.33), residues: 249 sheet: 0.63 (0.42), residues: 151 loop : -1.64 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 291 TYR 0.019 0.001 TYR A 242 PHE 0.018 0.002 PHE A 401 TRP 0.012 0.001 TRP A 282 HIS 0.003 0.001 HIS A 696 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 6348) covalent geometry : angle 0.57254 ( 8654) hydrogen bonds : bond 0.04317 ( 248) hydrogen bonds : angle 4.65645 ( 705) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 87 time to evaluate : 0.237 Fit side-chains REVERT: A 12 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7205 (mp0) REVERT: A 38 HIS cc_start: 0.7107 (OUTLIER) cc_final: 0.6431 (p90) REVERT: A 183 GLN cc_start: 0.5985 (mm-40) cc_final: 0.5520 (mt0) REVERT: A 270 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8477 (mt) REVERT: A 414 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7480 (mp10) REVERT: A 435 GLN cc_start: 0.7350 (pt0) cc_final: 0.6881 (mp10) REVERT: A 509 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7438 (mt) REVERT: A 600 ARG cc_start: 0.8022 (ptp-110) cc_final: 0.7790 (ptp-170) REVERT: A 734 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.6956 (tt) outliers start: 30 outliers final: 16 residues processed: 108 average time/residue: 0.4556 time to fit residues: 52.0537 Evaluate side-chains 104 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 734 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 15 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 52 optimal weight: 20.0000 chunk 39 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 571 ASN A 638 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.188214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.144583 restraints weight = 6597.367| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.42 r_work: 0.3306 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6348 Z= 0.139 Angle : 0.566 12.246 8654 Z= 0.304 Chirality : 0.043 0.152 965 Planarity : 0.003 0.036 1047 Dihedral : 12.513 75.980 943 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 5.00 % Allowed : 19.84 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.31), residues: 715 helix: 1.19 (0.33), residues: 250 sheet: 0.53 (0.42), residues: 155 loop : -1.56 (0.31), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 291 TYR 0.017 0.001 TYR A 242 PHE 0.013 0.001 PHE A 86 TRP 0.012 0.001 TRP A 282 HIS 0.003 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 6348) covalent geometry : angle 0.56587 ( 8654) hydrogen bonds : bond 0.04090 ( 248) hydrogen bonds : angle 4.60061 ( 705) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 85 time to evaluate : 0.219 Fit side-chains REVERT: A 12 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7302 (mp0) REVERT: A 38 HIS cc_start: 0.7092 (OUTLIER) cc_final: 0.6411 (p90) REVERT: A 73 MET cc_start: 0.6816 (mpt) cc_final: 0.6455 (OUTLIER) REVERT: A 183 GLN cc_start: 0.6033 (mm-40) cc_final: 0.5549 (mt0) REVERT: A 270 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8470 (mt) REVERT: A 414 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.7475 (mp10) REVERT: A 435 GLN cc_start: 0.7395 (pt0) cc_final: 0.6968 (mp10) REVERT: A 509 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7423 (mt) REVERT: A 600 ARG cc_start: 0.8037 (ptp-110) cc_final: 0.7797 (ptp-170) REVERT: A 734 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.6976 (tt) outliers start: 32 outliers final: 20 residues processed: 107 average time/residue: 0.4775 time to fit residues: 53.9629 Evaluate side-chains 108 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 663 GLN Chi-restraints excluded: chain A residue 734 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 6 optimal weight: 0.9980 chunk 36 optimal weight: 0.0670 chunk 4 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 57 optimal weight: 0.1980 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 571 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.189347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.134623 restraints weight = 6573.783| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.15 r_work: 0.3313 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6348 Z= 0.125 Angle : 0.554 11.865 8654 Z= 0.297 Chirality : 0.042 0.146 965 Planarity : 0.003 0.036 1047 Dihedral : 12.513 76.535 943 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.91 % Allowed : 21.09 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.31), residues: 715 helix: 1.28 (0.33), residues: 252 sheet: 0.55 (0.42), residues: 155 loop : -1.54 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 291 TYR 0.015 0.001 TYR A 242 PHE 0.017 0.001 PHE A 401 TRP 0.012 0.001 TRP A 282 HIS 0.004 0.001 HIS A 590 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 6348) covalent geometry : angle 0.55390 ( 8654) hydrogen bonds : bond 0.03836 ( 248) hydrogen bonds : angle 4.53754 ( 705) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.232 Fit side-chains REVERT: A 12 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7414 (mp0) REVERT: A 38 HIS cc_start: 0.7062 (OUTLIER) cc_final: 0.6310 (p90) REVERT: A 73 MET cc_start: 0.6797 (mpt) cc_final: 0.6456 (OUTLIER) REVERT: A 174 MET cc_start: 0.6951 (ttp) cc_final: 0.6163 (ptm) REVERT: A 183 GLN cc_start: 0.5923 (mm-40) cc_final: 0.5392 (mt0) REVERT: A 270 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8401 (mt) REVERT: A 414 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.7468 (mp10) REVERT: A 435 GLN cc_start: 0.7337 (pt0) cc_final: 0.6865 (mp10) REVERT: A 509 ILE cc_start: 0.7828 (OUTLIER) cc_final: 0.7388 (mt) REVERT: A 600 ARG cc_start: 0.8005 (ptp-110) cc_final: 0.7777 (ptp-170) REVERT: A 734 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.6940 (tt) outliers start: 25 outliers final: 17 residues processed: 102 average time/residue: 0.4890 time to fit residues: 52.3999 Evaluate side-chains 107 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 734 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 52 optimal weight: 20.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 571 ASN A 638 ASN A 701 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.186577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.139876 restraints weight = 6531.190| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.79 r_work: 0.3276 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6348 Z= 0.193 Angle : 0.626 12.541 8654 Z= 0.334 Chirality : 0.045 0.171 965 Planarity : 0.004 0.035 1047 Dihedral : 12.599 75.023 943 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.06 % Allowed : 20.94 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.30), residues: 715 helix: 1.00 (0.32), residues: 256 sheet: 0.57 (0.42), residues: 151 loop : -1.60 (0.31), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 291 TYR 0.019 0.002 TYR A 242 PHE 0.016 0.002 PHE A 86 TRP 0.008 0.001 TRP A 282 HIS 0.004 0.001 HIS A 696 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 6348) covalent geometry : angle 0.62562 ( 8654) hydrogen bonds : bond 0.04854 ( 248) hydrogen bonds : angle 4.71524 ( 705) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.232 Fit side-chains REVERT: A 12 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7308 (mp0) REVERT: A 38 HIS cc_start: 0.7177 (OUTLIER) cc_final: 0.6551 (p90) REVERT: A 183 GLN cc_start: 0.6021 (mm-40) cc_final: 0.5535 (mt0) REVERT: A 270 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8513 (mt) REVERT: A 414 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7252 (mp10) REVERT: A 435 GLN cc_start: 0.7375 (pt0) cc_final: 0.6856 (mp10) REVERT: A 509 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7512 (mt) REVERT: A 600 ARG cc_start: 0.8065 (ptp-110) cc_final: 0.7839 (ptp-170) REVERT: A 734 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.6999 (tt) outliers start: 26 outliers final: 16 residues processed: 104 average time/residue: 0.4352 time to fit residues: 47.7560 Evaluate side-chains 105 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 734 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 46 optimal weight: 0.0000 chunk 71 optimal weight: 20.0000 chunk 65 optimal weight: 0.4980 chunk 9 optimal weight: 2.9990 chunk 49 optimal weight: 0.0980 chunk 17 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 571 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.189121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.144866 restraints weight = 6494.563| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.20 r_work: 0.3327 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6348 Z= 0.129 Angle : 0.562 12.696 8654 Z= 0.301 Chirality : 0.042 0.147 965 Planarity : 0.003 0.034 1047 Dihedral : 12.523 76.455 943 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.75 % Allowed : 21.72 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.31), residues: 715 helix: 1.21 (0.33), residues: 252 sheet: 0.68 (0.42), residues: 151 loop : -1.58 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 291 TYR 0.015 0.001 TYR A 242 PHE 0.019 0.001 PHE A 401 TRP 0.013 0.001 TRP A 282 HIS 0.003 0.001 HIS A 590 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 6348) covalent geometry : angle 0.56216 ( 8654) hydrogen bonds : bond 0.03857 ( 248) hydrogen bonds : angle 4.58648 ( 705) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2571.18 seconds wall clock time: 44 minutes 18.86 seconds (2658.86 seconds total)