Starting phenix.real_space_refine on Fri May 9 21:30:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j5w_61155/05_2025/9j5w_61155.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j5w_61155/05_2025/9j5w_61155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j5w_61155/05_2025/9j5w_61155.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j5w_61155/05_2025/9j5w_61155.map" model { file = "/net/cci-nas-00/data/ceres_data/9j5w_61155/05_2025/9j5w_61155.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j5w_61155/05_2025/9j5w_61155.cif" } resolution = 3.2 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= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Br 2 7.06 5 S 22 5.16 5 C 2552 2.51 5 N 671 2.21 5 O 686 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3933 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 3911 Classifications: {'peptide': 515} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 26, 'TRANS': 488} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'R75': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.05, per 1000 atoms: 0.78 Number of scatterers: 3933 At special positions: 0 Unit cell: (107.1, 68, 68.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Br 2 34.99 S 22 16.00 O 686 8.00 N 671 7.00 C 2552 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 139 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 492.6 milliseconds 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 944 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 2 sheets defined 83.3% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 3.600A pdb=" N LEU A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 37 Proline residue: A 27 - end of helix removed outlier: 4.167A pdb=" N TRP A 30 " --> pdb=" O THR A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 42 removed outlier: 3.533A pdb=" N ALA A 42 " --> pdb=" O GLU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 68 through 77 Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.595A pdb=" N ILE A 99 " --> pdb=" O TRP A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 130 through 136 Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 143 through 171 removed outlier: 3.999A pdb=" N MET A 147 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 191 Processing helix chain 'A' and resid 195 through 224 Processing helix chain 'A' and resid 226 through 228 No H-bonds generated for 'chain 'A' and resid 226 through 228' Processing helix chain 'A' and resid 229 through 255 removed outlier: 3.599A pdb=" N PHE A 241 " --> pdb=" O ASN A 237 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 267 through 277 removed outlier: 4.189A pdb=" N LEU A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N TRP A 277 " --> pdb=" O PHE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 290 removed outlier: 3.588A pdb=" N LEU A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 306 Processing helix chain 'A' and resid 308 through 314 removed outlier: 4.418A pdb=" N THR A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 327 Processing helix chain 'A' and resid 332 through 343 removed outlier: 4.073A pdb=" N LEU A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLY A 338 " --> pdb=" O GLY A 334 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 343 " --> pdb=" O THR A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 368 removed outlier: 3.903A pdb=" N LEU A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ARG A 349 " --> pdb=" O GLY A 345 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE A 360 " --> pdb=" O CYS A 356 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY A 361 " --> pdb=" O TRP A 357 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 366 " --> pdb=" O PHE A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 404 removed outlier: 3.905A pdb=" N GLY A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 390 " --> pdb=" O GLY A 386 " (cutoff:3.500A) Proline residue: A 391 - end of helix removed outlier: 3.606A pdb=" N LEU A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 398 " --> pdb=" O MET A 394 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N SER A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 426 removed outlier: 4.364A pdb=" N GLN A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA A 410 " --> pdb=" O ARG A 406 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) Proline residue: A 416 - end of helix removed outlier: 4.146A pdb=" N ILE A 424 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 460 removed outlier: 3.788A pdb=" N ALA A 438 " --> pdb=" O ARG A 434 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ALA A 447 " --> pdb=" O GLY A 443 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 450 " --> pdb=" O GLY A 446 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE A 454 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SER A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU A 458 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 459 " --> pdb=" O PHE A 455 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'A' and resid 464 through 486 removed outlier: 3.519A pdb=" N ILE A 481 " --> pdb=" O ARG A 477 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 482 " --> pdb=" O GLY A 478 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 483 " --> pdb=" O GLY A 479 " (cutoff:3.500A) Proline residue: A 484 - end of helix Processing helix chain 'A' and resid 487 through 492 removed outlier: 3.708A pdb=" N VAL A 491 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 511 removed outlier: 4.418A pdb=" N LEU A 498 " --> pdb=" O SER A 494 " (cutoff:3.500A) Proline residue: A 505 - end of helix Processing helix chain 'A' and resid 512 through 515 removed outlier: 3.621A pdb=" N LEU A 515 " --> pdb=" O ALA A 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 512 through 515' Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 91 251 hydrogen bonds defined for protein. 735 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.07 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 901 1.33 - 1.48: 1391 1.48 - 1.63: 1700 1.63 - 1.79: 0 1.79 - 1.94: 36 Bond restraints: 4028 Sorted by residual: bond pdb=" CAO R75 A 601 " pdb=" CAS R75 A 601 " ideal model delta sigma weight residual 1.382 1.574 -0.192 2.00e-02 2.50e+03 9.26e+01 bond pdb=" CAP R75 A 601 " pdb=" CAV R75 A 601 " ideal model delta sigma weight residual 1.396 1.574 -0.178 2.00e-02 2.50e+03 7.94e+01 bond pdb=" CAA R75 A 601 " pdb=" CAB R75 A 601 " ideal model delta sigma weight residual 1.378 1.525 -0.147 2.00e-02 2.50e+03 5.38e+01 bond pdb=" CAD R75 A 601 " pdb=" CAE R75 A 601 " ideal model delta sigma weight residual 1.382 1.526 -0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" CAE R75 A 601 " pdb=" CAF R75 A 601 " ideal model delta sigma weight residual 1.389 1.525 -0.136 2.00e-02 2.50e+03 4.65e+01 ... (remaining 4023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 5396 1.91 - 3.83: 80 3.83 - 5.74: 23 5.74 - 7.65: 4 7.65 - 9.57: 1 Bond angle restraints: 5504 Sorted by residual: angle pdb=" CAQ R75 A 601 " pdb=" CAM R75 A 601 " pdb=" OAN R75 A 601 " ideal model delta sigma weight residual 116.30 125.87 -9.57 3.00e+00 1.11e-01 1.02e+01 angle pdb=" N GLN A 245 " pdb=" CA GLN A 245 " pdb=" C GLN A 245 " ideal model delta sigma weight residual 111.07 107.73 3.34 1.07e+00 8.73e-01 9.72e+00 angle pdb=" C GLY A 14 " pdb=" N ARG A 15 " pdb=" CA ARG A 15 " ideal model delta sigma weight residual 121.54 125.99 -4.45 1.91e+00 2.74e-01 5.43e+00 angle pdb=" CAS R75 A 601 " pdb=" CAO R75 A 601 " pdb=" OAN R75 A 601 " ideal model delta sigma weight residual 125.82 132.40 -6.58 3.00e+00 1.11e-01 4.81e+00 angle pdb=" N ARG A 15 " pdb=" CA ARG A 15 " pdb=" C ARG A 15 " ideal model delta sigma weight residual 110.80 115.43 -4.63 2.13e+00 2.20e-01 4.72e+00 ... (remaining 5499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 2149 17.86 - 35.71: 162 35.71 - 53.57: 31 53.57 - 71.43: 5 71.43 - 89.29: 2 Dihedral angle restraints: 2349 sinusoidal: 884 harmonic: 1465 Sorted by residual: dihedral pdb=" CB CYS A 49 " pdb=" SG CYS A 49 " pdb=" SG CYS A 116 " pdb=" CB CYS A 116 " ideal model delta sinusoidal sigma weight residual -86.00 -142.01 56.01 1 1.00e+01 1.00e-02 4.23e+01 dihedral pdb=" CA GLN A 87 " pdb=" C GLN A 87 " pdb=" N CYS A 88 " pdb=" CA CYS A 88 " ideal model delta harmonic sigma weight residual -180.00 -164.43 -15.57 0 5.00e+00 4.00e-02 9.70e+00 dihedral pdb=" CB MET A 234 " pdb=" CG MET A 234 " pdb=" SD MET A 234 " pdb=" CE MET A 234 " ideal model delta sinusoidal sigma weight residual 180.00 127.66 52.34 3 1.50e+01 4.44e-03 9.11e+00 ... (remaining 2346 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 394 0.026 - 0.052: 147 0.052 - 0.078: 72 0.078 - 0.103: 31 0.103 - 0.129: 5 Chirality restraints: 649 Sorted by residual: chirality pdb=" CA GLN A 245 " pdb=" N GLN A 245 " pdb=" C GLN A 245 " pdb=" CB GLN A 245 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CA VAL A 44 " pdb=" N VAL A 44 " pdb=" C VAL A 44 " pdb=" CB VAL A 44 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.52e-01 chirality pdb=" CA VAL A 426 " pdb=" N VAL A 426 " pdb=" C VAL A 426 " pdb=" CB VAL A 426 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.31e-01 ... (remaining 646 not shown) Planarity restraints: 691 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 279 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO A 280 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 280 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 280 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 230 " -0.026 5.00e-02 4.00e+02 3.87e-02 2.40e+00 pdb=" N PRO A 231 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 231 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 231 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 3 " 0.021 5.00e-02 4.00e+02 3.12e-02 1.56e+00 pdb=" N PRO A 4 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 4 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 4 " 0.018 5.00e-02 4.00e+02 ... (remaining 688 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 24 2.67 - 3.23: 3813 3.23 - 3.79: 5929 3.79 - 4.34: 7639 4.34 - 4.90: 12844 Nonbonded interactions: 30249 Sorted by model distance: nonbonded pdb=" O PRO A 52 " pdb=" OG SER A 59 " model vdw 2.114 3.040 nonbonded pdb=" O ALA A 42 " pdb=" NH1 ARG A 145 " model vdw 2.283 3.120 nonbonded pdb=" OH TYR A 122 " pdb=" OD1 ASP A 136 " model vdw 2.350 3.040 nonbonded pdb=" O LEU A 54 " pdb=" NE2 GLN A 60 " model vdw 2.361 3.120 nonbonded pdb=" NH2 ARG A 9 " pdb=" O GLU A 311 " model vdw 2.383 3.120 ... (remaining 30244 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.970 Find NCS groups from input model: 0.030 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: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 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 : 0.008 0.192 4030 Z= 0.405 Angle : 0.622 9.567 5508 Z= 0.315 Chirality : 0.036 0.129 649 Planarity : 0.005 0.047 691 Dihedral : 13.101 89.286 1399 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.17 % Favored : 98.64 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: 1.27 (0.36), residues: 513 helix: 1.25 (0.27), residues: 361 sheet: None (None), residues: 0 loop : 0.06 (0.49), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 278 HIS 0.004 0.001 HIS A 86 PHE 0.016 0.001 PHE A 204 TYR 0.009 0.001 TYR A 275 ARG 0.004 0.000 ARG A 321 Details of bonding type rmsd hydrogen bonds : bond 0.20592 ( 251) hydrogen bonds : angle 6.03910 ( 735) SS BOND : bond 0.00137 ( 2) SS BOND : angle 0.78315 ( 4) covalent geometry : bond 0.00805 ( 4028) covalent geometry : angle 0.62172 ( 5504) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.440 Fit side-chains REVERT: A 77 ILE cc_start: 0.7538 (mm) cc_final: 0.7278 (mm) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1785 time to fit residues: 12.4983 Evaluate side-chains 51 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 13 optimal weight: 0.0370 chunk 26 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.197465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.145598 restraints weight = 4186.127| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.45 r_work: 0.3625 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4030 Z= 0.133 Angle : 0.594 8.997 5508 Z= 0.291 Chirality : 0.039 0.122 649 Planarity : 0.005 0.045 691 Dihedral : 4.083 22.035 556 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.39 % Favored : 99.42 % Rotamer: Outliers : 0.48 % Allowed : 5.31 % Favored : 94.20 % 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: 1.41 (0.36), residues: 513 helix: 1.43 (0.26), residues: 365 sheet: None (None), residues: 0 loop : -0.17 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 258 HIS 0.002 0.001 HIS A 47 PHE 0.015 0.001 PHE A 204 TYR 0.011 0.001 TYR A 275 ARG 0.006 0.000 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.05407 ( 251) hydrogen bonds : angle 4.47611 ( 735) SS BOND : bond 0.00294 ( 2) SS BOND : angle 0.79985 ( 4) covalent geometry : bond 0.00267 ( 4028) covalent geometry : angle 0.59418 ( 5504) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.414 Fit side-chains REVERT: A 389 ASP cc_start: 0.7203 (t70) cc_final: 0.6995 (t0) outliers start: 2 outliers final: 1 residues processed: 60 average time/residue: 0.1529 time to fit residues: 11.7955 Evaluate side-chains 48 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 22 optimal weight: 0.0030 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.195208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.145346 restraints weight = 4208.609| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.42 r_work: 0.3606 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4030 Z= 0.126 Angle : 0.563 8.018 5508 Z= 0.276 Chirality : 0.039 0.135 649 Planarity : 0.004 0.044 691 Dihedral : 3.984 19.020 556 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.78 % Favored : 99.03 % Rotamer: Outliers : 0.48 % Allowed : 9.42 % Favored : 90.10 % 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: 1.49 (0.36), residues: 513 helix: 1.53 (0.27), residues: 365 sheet: None (None), residues: 0 loop : -0.26 (0.49), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 258 HIS 0.003 0.001 HIS A 47 PHE 0.015 0.001 PHE A 204 TYR 0.012 0.001 TYR A 275 ARG 0.004 0.000 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.05120 ( 251) hydrogen bonds : angle 4.26853 ( 735) SS BOND : bond 0.00301 ( 2) SS BOND : angle 0.74542 ( 4) covalent geometry : bond 0.00260 ( 4028) covalent geometry : angle 0.56239 ( 5504) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.399 Fit side-chains REVERT: A 28 ILE cc_start: 0.6675 (mm) cc_final: 0.6295 (mm) REVERT: A 89 LEU cc_start: 0.8479 (mt) cc_final: 0.8096 (mt) REVERT: A 433 LEU cc_start: 0.6703 (tt) cc_final: 0.5739 (mt) REVERT: A 434 ARG cc_start: 0.8173 (mmm-85) cc_final: 0.7736 (mmm-85) outliers start: 2 outliers final: 2 residues processed: 49 average time/residue: 0.1775 time to fit residues: 10.8687 Evaluate side-chains 47 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 167 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 23 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 6 optimal weight: 0.3980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.189882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.139513 restraints weight = 4205.520| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.40 r_work: 0.3574 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4030 Z= 0.150 Angle : 0.593 8.471 5508 Z= 0.291 Chirality : 0.040 0.151 649 Planarity : 0.005 0.047 691 Dihedral : 4.135 18.534 556 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.17 % Favored : 98.64 % Rotamer: Outliers : 0.97 % Allowed : 12.08 % Favored : 86.96 % 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: 1.47 (0.37), residues: 513 helix: 1.48 (0.27), residues: 366 sheet: None (None), residues: 0 loop : -0.19 (0.50), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 258 HIS 0.003 0.001 HIS A 47 PHE 0.015 0.002 PHE A 202 TYR 0.016 0.002 TYR A 275 ARG 0.005 0.000 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.05855 ( 251) hydrogen bonds : angle 4.32973 ( 735) SS BOND : bond 0.00539 ( 2) SS BOND : angle 1.02144 ( 4) covalent geometry : bond 0.00337 ( 4028) covalent geometry : angle 0.59213 ( 5504) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6975 (pm20) REVERT: A 390 LEU cc_start: 0.7009 (tt) cc_final: 0.6686 (mt) REVERT: A 434 ARG cc_start: 0.8227 (mmm-85) cc_final: 0.7672 (mmm-85) outliers start: 4 outliers final: 4 residues processed: 59 average time/residue: 0.1795 time to fit residues: 13.1225 Evaluate side-chains 54 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 388 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 34 optimal weight: 8.9990 chunk 17 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.190235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.139047 restraints weight = 4260.960| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.44 r_work: 0.3552 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4030 Z= 0.133 Angle : 0.573 10.190 5508 Z= 0.280 Chirality : 0.039 0.137 649 Planarity : 0.004 0.043 691 Dihedral : 4.094 20.461 556 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.58 % Favored : 99.22 % Rotamer: Outliers : 0.48 % Allowed : 13.53 % Favored : 85.99 % 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: 1.48 (0.37), residues: 513 helix: 1.49 (0.27), residues: 366 sheet: None (None), residues: 0 loop : -0.19 (0.50), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 258 HIS 0.003 0.001 HIS A 47 PHE 0.016 0.002 PHE A 204 TYR 0.013 0.001 TYR A 275 ARG 0.004 0.000 ARG A 321 Details of bonding type rmsd hydrogen bonds : bond 0.05300 ( 251) hydrogen bonds : angle 4.23230 ( 735) SS BOND : bond 0.00378 ( 2) SS BOND : angle 0.88996 ( 4) covalent geometry : bond 0.00288 ( 4028) covalent geometry : angle 0.57241 ( 5504) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 9 ARG cc_start: 0.6343 (ptm160) cc_final: 0.5900 (ttt90) REVERT: A 89 LEU cc_start: 0.8434 (mt) cc_final: 0.8190 (mt) REVERT: A 390 LEU cc_start: 0.7041 (tt) cc_final: 0.6687 (mt) REVERT: A 434 ARG cc_start: 0.8208 (mmm-85) cc_final: 0.7670 (mmm-85) outliers start: 2 outliers final: 2 residues processed: 62 average time/residue: 0.1696 time to fit residues: 13.1847 Evaluate side-chains 58 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 167 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 9 optimal weight: 0.8980 chunk 2 optimal weight: 0.3980 chunk 10 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.193380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.143066 restraints weight = 4222.185| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.43 r_work: 0.3582 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4030 Z= 0.129 Angle : 0.568 8.973 5508 Z= 0.277 Chirality : 0.039 0.137 649 Planarity : 0.004 0.044 691 Dihedral : 4.076 21.672 556 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.97 % Favored : 98.83 % Rotamer: Outliers : 1.21 % Allowed : 13.53 % Favored : 85.27 % 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: 1.49 (0.37), residues: 513 helix: 1.48 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -0.12 (0.51), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 357 HIS 0.003 0.001 HIS A 47 PHE 0.016 0.002 PHE A 204 TYR 0.013 0.001 TYR A 275 ARG 0.004 0.000 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.05185 ( 251) hydrogen bonds : angle 4.19123 ( 735) SS BOND : bond 0.00449 ( 2) SS BOND : angle 0.80636 ( 4) covalent geometry : bond 0.00274 ( 4028) covalent geometry : angle 0.56777 ( 5504) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.372 Fit side-chains REVERT: A 9 ARG cc_start: 0.6478 (ptm160) cc_final: 0.6116 (ttt90) REVERT: A 390 LEU cc_start: 0.7122 (tt) cc_final: 0.6727 (mt) outliers start: 5 outliers final: 5 residues processed: 64 average time/residue: 0.1772 time to fit residues: 14.0887 Evaluate side-chains 57 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 433 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 4 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 17 optimal weight: 0.0670 chunk 20 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.191141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.141514 restraints weight = 4160.588| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.36 r_work: 0.3557 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4030 Z= 0.130 Angle : 0.583 8.234 5508 Z= 0.284 Chirality : 0.039 0.136 649 Planarity : 0.004 0.043 691 Dihedral : 4.088 22.830 556 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.78 % Favored : 99.03 % Rotamer: Outliers : 1.21 % Allowed : 13.29 % Favored : 85.51 % 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: 1.43 (0.38), residues: 513 helix: 1.42 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -0.13 (0.52), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 357 HIS 0.003 0.001 HIS A 47 PHE 0.016 0.002 PHE A 204 TYR 0.013 0.001 TYR A 275 ARG 0.004 0.000 ARG A 321 Details of bonding type rmsd hydrogen bonds : bond 0.05160 ( 251) hydrogen bonds : angle 4.17171 ( 735) SS BOND : bond 0.00588 ( 2) SS BOND : angle 1.28116 ( 4) covalent geometry : bond 0.00281 ( 4028) covalent geometry : angle 0.58240 ( 5504) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.434 Fit side-chains REVERT: A 9 ARG cc_start: 0.6749 (ptm160) cc_final: 0.6428 (ttt90) REVERT: A 89 LEU cc_start: 0.8756 (mt) cc_final: 0.8471 (mt) REVERT: A 390 LEU cc_start: 0.7195 (tt) cc_final: 0.6728 (mt) outliers start: 5 outliers final: 5 residues processed: 58 average time/residue: 0.1781 time to fit residues: 12.9641 Evaluate side-chains 55 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 433 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 40 optimal weight: 0.0170 chunk 44 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.189987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.139950 restraints weight = 4157.649| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.38 r_work: 0.3574 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4030 Z= 0.126 Angle : 0.573 7.696 5508 Z= 0.279 Chirality : 0.038 0.132 649 Planarity : 0.004 0.042 691 Dihedral : 4.080 24.727 556 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.56 % Favored : 98.25 % Rotamer: Outliers : 1.45 % Allowed : 13.77 % Favored : 84.78 % 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: 1.46 (0.38), residues: 513 helix: 1.45 (0.28), residues: 370 sheet: None (None), residues: 0 loop : -0.16 (0.52), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 357 HIS 0.002 0.000 HIS A 47 PHE 0.016 0.002 PHE A 204 TYR 0.013 0.001 TYR A 275 ARG 0.004 0.000 ARG A 321 Details of bonding type rmsd hydrogen bonds : bond 0.05033 ( 251) hydrogen bonds : angle 4.13170 ( 735) SS BOND : bond 0.00302 ( 2) SS BOND : angle 1.74670 ( 4) covalent geometry : bond 0.00268 ( 4028) covalent geometry : angle 0.57087 ( 5504) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.412 Fit side-chains REVERT: A 9 ARG cc_start: 0.6729 (ptm160) cc_final: 0.6366 (ttt90) REVERT: A 321 ARG cc_start: 0.6987 (tpp80) cc_final: 0.6721 (ttm-80) REVERT: A 390 LEU cc_start: 0.7200 (tt) cc_final: 0.6708 (mt) outliers start: 6 outliers final: 6 residues processed: 58 average time/residue: 0.1702 time to fit residues: 12.4296 Evaluate side-chains 56 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 433 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 6 optimal weight: 0.0170 chunk 9 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 26 optimal weight: 0.0570 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 48 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.194938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.145737 restraints weight = 4116.592| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.36 r_work: 0.3618 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4030 Z= 0.117 Angle : 0.563 7.620 5508 Z= 0.274 Chirality : 0.037 0.124 649 Planarity : 0.004 0.042 691 Dihedral : 4.031 25.758 556 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.36 % Favored : 98.44 % Rotamer: Outliers : 1.45 % Allowed : 14.01 % Favored : 84.54 % 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: 1.57 (0.38), residues: 513 helix: 1.54 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -0.16 (0.53), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 357 HIS 0.002 0.000 HIS A 47 PHE 0.018 0.001 PHE A 204 TYR 0.012 0.001 TYR A 275 ARG 0.003 0.000 ARG A 321 Details of bonding type rmsd hydrogen bonds : bond 0.04495 ( 251) hydrogen bonds : angle 4.04395 ( 735) SS BOND : bond 0.00276 ( 2) SS BOND : angle 1.55273 ( 4) covalent geometry : bond 0.00237 ( 4028) covalent geometry : angle 0.56198 ( 5504) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.390 Fit side-chains REVERT: A 321 ARG cc_start: 0.7097 (tpp80) cc_final: 0.6859 (ttm-80) REVERT: A 390 LEU cc_start: 0.7263 (tt) cc_final: 0.6757 (mt) outliers start: 6 outliers final: 5 residues processed: 58 average time/residue: 0.1669 time to fit residues: 12.1914 Evaluate side-chains 55 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 433 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 12 optimal weight: 0.0470 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 11 optimal weight: 0.0970 chunk 29 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.192908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.143593 restraints weight = 4083.848| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.34 r_work: 0.3615 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4030 Z= 0.116 Angle : 0.558 7.411 5508 Z= 0.272 Chirality : 0.038 0.125 649 Planarity : 0.004 0.042 691 Dihedral : 4.009 26.869 556 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.36 % Favored : 98.44 % Rotamer: Outliers : 1.21 % Allowed : 14.73 % Favored : 84.06 % 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: 1.61 (0.38), residues: 513 helix: 1.59 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -0.19 (0.52), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 357 HIS 0.002 0.000 HIS A 47 PHE 0.016 0.001 PHE A 204 TYR 0.012 0.001 TYR A 275 ARG 0.003 0.000 ARG A 321 Details of bonding type rmsd hydrogen bonds : bond 0.04535 ( 251) hydrogen bonds : angle 4.02080 ( 735) SS BOND : bond 0.00244 ( 2) SS BOND : angle 1.46841 ( 4) covalent geometry : bond 0.00237 ( 4028) covalent geometry : angle 0.55684 ( 5504) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.438 Fit side-chains REVERT: A 9 ARG cc_start: 0.6796 (ptm160) cc_final: 0.6401 (ttt90) REVERT: A 117 GLU cc_start: 0.7484 (mt-10) cc_final: 0.6959 (mm-30) REVERT: A 321 ARG cc_start: 0.7079 (tpp80) cc_final: 0.6846 (ttm-80) REVERT: A 390 LEU cc_start: 0.7148 (tt) cc_final: 0.6778 (mt) outliers start: 5 outliers final: 5 residues processed: 57 average time/residue: 0.1759 time to fit residues: 12.5818 Evaluate side-chains 56 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 433 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 26 optimal weight: 0.2980 chunk 25 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 5 optimal weight: 0.0370 chunk 3 optimal weight: 0.5980 chunk 8 optimal weight: 8.9990 chunk 50 optimal weight: 0.5980 chunk 9 optimal weight: 0.0040 overall best weight: 0.3070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.195690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.147477 restraints weight = 3982.000| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.28 r_work: 0.3638 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4030 Z= 0.110 Angle : 0.549 7.419 5508 Z= 0.267 Chirality : 0.037 0.118 649 Planarity : 0.004 0.041 691 Dihedral : 3.950 28.236 556 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.78 % Favored : 99.03 % Rotamer: Outliers : 1.45 % Allowed : 14.49 % Favored : 84.06 % 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: 1.76 (0.38), residues: 513 helix: 1.70 (0.28), residues: 370 sheet: None (None), residues: 0 loop : -0.16 (0.53), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 357 HIS 0.002 0.000 HIS A 47 PHE 0.018 0.001 PHE A 204 TYR 0.012 0.001 TYR A 275 ARG 0.003 0.000 ARG A 321 Details of bonding type rmsd hydrogen bonds : bond 0.03998 ( 251) hydrogen bonds : angle 3.93914 ( 735) SS BOND : bond 0.00195 ( 2) SS BOND : angle 1.31441 ( 4) covalent geometry : bond 0.00217 ( 4028) covalent geometry : angle 0.54805 ( 5504) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2378.36 seconds wall clock time: 41 minutes 47.80 seconds (2507.80 seconds total)