Starting phenix.real_space_refine on Wed Mar 5 22:32:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j5w_61155/03_2025/9j5w_61155.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j5w_61155/03_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_61155/03_2025/9j5w_61155.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j5w_61155/03_2025/9j5w_61155.map" model { file = "/net/cci-nas-00/data/ceres_data/9j5w_61155/03_2025/9j5w_61155.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j5w_61155/03_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-5624/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: 3.03, per 1000 atoms: 0.77 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: 0.96 Conformation dependent library (CDL) restraints added in 482.4 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: 0.42 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: 1.05 Time building geometry restraints manager: 1.14 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: 0.960 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: 13.940 Find NCS groups from input model: 0.040 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.000 ------------------------------------------------------------------------------- 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 4028 Z= 0.533 Angle : 0.622 9.567 5504 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 *********************** 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 : 0.398 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: 0.1727 time to fit residues: 12.0871 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 : 0.401 ------------------------------------------------------------------------------- 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 = 0.197464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.145598 restraints weight = 4186.136| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.45 r_work: 0.3626 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 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 4028 Z= 0.176 Angle : 0.594 8.997 5504 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 *********************** 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 : 0.406 Fit side-chains REVERT: A 389 ASP cc_start: 0.7197 (t70) cc_final: 0.6991 (t0) outliers start: 2 outliers final: 1 residues processed: 60 average time/residue: 0.1511 time to fit residues: 11.6238 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 : 0.371 ------------------------------------------------------------------------------- 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: 1.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 0.4980 chunk 43 optimal weight: 0.7980 chunk 22 optimal weight: 0.0870 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 0.2980 chunk 41 optimal weight: 5.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 = 0.4263 r_free = 0.4263 target = 0.196551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.147013 restraints weight = 4213.904| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.42 r_work: 0.3622 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4028 Z= 0.159 Angle : 0.554 7.947 5504 Z= 0.272 Chirality : 0.038 0.130 649 Planarity : 0.004 0.043 691 Dihedral : 3.959 19.576 556 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.67 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: 1.53 (0.36), residues: 513 helix: 1.55 (0.27), residues: 365 sheet: None (None), residues: 0 loop : -0.24 (0.49), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 258 HIS 0.003 0.001 HIS A 47 PHE 0.016 0.001 PHE A 204 TYR 0.011 0.001 TYR A 275 ARG 0.004 0.000 ARG A 145 *********************** 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 52 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.371 Fit side-chains REVERT: A 28 ILE cc_start: 0.6620 (mm) cc_final: 0.6244 (mm) REVERT: A 89 LEU cc_start: 0.8436 (mt) cc_final: 0.8042 (mt) REVERT: A 434 ARG cc_start: 0.8161 (mmm-85) cc_final: 0.7783 (mmm-85) outliers start: 2 outliers final: 2 residues processed: 52 average time/residue: 0.1791 time to fit residues: 11.6956 Evaluate side-chains 50 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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: 1.9990 chunk 50 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 5 optimal weight: 0.0970 chunk 44 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.4249 r_free = 0.4249 target = 0.195134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.145641 restraints weight = 4196.354| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.41 r_work: 0.3603 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4028 Z= 0.165 Angle : 0.554 8.190 5504 Z= 0.269 Chirality : 0.038 0.133 649 Planarity : 0.004 0.044 691 Dihedral : 3.957 19.252 556 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.17 % Favored : 98.64 % Rotamer: Outliers : 0.72 % Allowed : 10.63 % Favored : 88.65 % 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: 1.62 (0.37), residues: 513 helix: 1.61 (0.27), residues: 366 sheet: None (None), residues: 0 loop : -0.19 (0.49), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 258 HIS 0.002 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 *********************** 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 53 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 28 ILE cc_start: 0.6675 (mm) cc_final: 0.6305 (mm) outliers start: 3 outliers final: 3 residues processed: 53 average time/residue: 0.1765 time to fit residues: 11.7154 Evaluate side-chains 50 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 433 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 30 optimal weight: 0.7980 chunk 32 optimal weight: 8.9990 chunk 12 optimal weight: 0.0270 chunk 2 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 17 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.6438 ------------------------------------------------------------------------------- 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 = 0.4244 r_free = 0.4244 target = 0.194833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.145121 restraints weight = 4281.630| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.43 r_work: 0.3575 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4028 Z= 0.168 Angle : 0.553 8.816 5504 Z= 0.268 Chirality : 0.038 0.132 649 Planarity : 0.004 0.044 691 Dihedral : 3.979 19.585 556 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.78 % Favored : 99.03 % 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: 1.71 (0.37), residues: 513 helix: 1.67 (0.27), residues: 366 sheet: None (None), residues: 0 loop : -0.11 (0.50), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 258 HIS 0.003 0.001 HIS A 47 PHE 0.015 0.002 PHE A 204 TYR 0.013 0.001 TYR A 275 ARG 0.004 0.000 ARG A 145 *********************** 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 61 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 89 LEU cc_start: 0.8399 (mt) cc_final: 0.8176 (mt) REVERT: A 390 LEU cc_start: 0.7047 (tt) cc_final: 0.6753 (mt) outliers start: 4 outliers final: 3 residues processed: 61 average time/residue: 0.1471 time to fit residues: 11.5622 Evaluate side-chains 60 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 8 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.4213 r_free = 0.4213 target = 0.191842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.142342 restraints weight = 4220.520| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.39 r_work: 0.3551 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4028 Z= 0.203 Angle : 0.588 7.079 5504 Z= 0.290 Chirality : 0.040 0.140 649 Planarity : 0.005 0.045 691 Dihedral : 4.038 20.946 556 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.17 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: 1.58 (0.37), residues: 513 helix: 1.54 (0.28), residues: 367 sheet: None (None), residues: 0 loop : -0.09 (0.51), residues: 146 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 0.002 PHE A 204 TYR 0.014 0.001 TYR A 275 ARG 0.004 0.000 ARG A 145 *********************** 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 63 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.410 Fit side-chains REVERT: A 9 ARG cc_start: 0.6278 (ptm160) cc_final: 0.5921 (ttt90) REVERT: A 390 LEU cc_start: 0.7139 (tt) cc_final: 0.6790 (mt) outliers start: 5 outliers final: 5 residues processed: 63 average time/residue: 0.1641 time to fit residues: 13.0580 Evaluate side-chains 59 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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: 3.9990 chunk 26 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 30 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 22 optimal weight: 0.0370 chunk 25 optimal weight: 0.9990 overall best weight: 0.5860 ------------------------------------------------------------------------------- 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 = 0.4214 r_free = 0.4214 target = 0.191915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.143005 restraints weight = 4173.014| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.35 r_work: 0.3572 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4028 Z= 0.165 Angle : 0.566 6.815 5504 Z= 0.279 Chirality : 0.038 0.130 649 Planarity : 0.004 0.043 691 Dihedral : 4.024 22.036 556 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.58 % Favored : 99.22 % Rotamer: Outliers : 1.45 % Allowed : 13.29 % 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: 1.64 (0.37), residues: 513 helix: 1.60 (0.28), residues: 367 sheet: None (None), residues: 0 loop : -0.12 (0.51), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 357 HIS 0.004 0.001 HIS A 47 PHE 0.016 0.001 PHE A 204 TYR 0.012 0.001 TYR A 275 ARG 0.004 0.000 ARG A 321 *********************** 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 60 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.421 Fit side-chains REVERT: A 9 ARG cc_start: 0.6353 (ptm160) cc_final: 0.5969 (ttt90) REVERT: A 89 LEU cc_start: 0.8672 (mt) cc_final: 0.8442 (mt) REVERT: A 390 LEU cc_start: 0.7164 (tt) cc_final: 0.6820 (mt) outliers start: 6 outliers final: 5 residues processed: 59 average time/residue: 0.1520 time to fit residues: 11.5155 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 : 0.370 ------------------------------------------------------------------------------- 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: 0.0070 chunk 44 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 11 optimal weight: 0.0060 chunk 10 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 overall best weight: 0.5416 ------------------------------------------------------------------------------- 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 = 0.4232 r_free = 0.4232 target = 0.193567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.144365 restraints weight = 4176.042| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.39 r_work: 0.3580 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4028 Z= 0.159 Angle : 0.573 10.820 5504 Z= 0.275 Chirality : 0.038 0.126 649 Planarity : 0.004 0.043 691 Dihedral : 4.000 23.405 556 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.17 % Favored : 98.64 % Rotamer: Outliers : 0.97 % Allowed : 14.49 % 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: 1.65 (0.38), residues: 513 helix: 1.59 (0.28), residues: 370 sheet: None (None), residues: 0 loop : -0.10 (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 0.001 PHE A 204 TYR 0.012 0.001 TYR A 275 ARG 0.003 0.000 ARG A 321 *********************** 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 60 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.435 Fit side-chains REVERT: A 9 ARG cc_start: 0.6347 (ptm160) cc_final: 0.6012 (ttt90) REVERT: A 89 LEU cc_start: 0.8674 (mt) cc_final: 0.8402 (mt) REVERT: A 390 LEU cc_start: 0.7225 (tt) cc_final: 0.6789 (mt) outliers start: 4 outliers final: 4 residues processed: 60 average time/residue: 0.1715 time to fit residues: 13.0627 Evaluate side-chains 57 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 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: 0.0570 chunk 9 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 = 0.4218 r_free = 0.4218 target = 0.192199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.143585 restraints weight = 4153.294| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.35 r_work: 0.3604 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4028 Z= 0.163 Angle : 0.576 10.095 5504 Z= 0.279 Chirality : 0.038 0.126 649 Planarity : 0.004 0.043 691 Dihedral : 4.007 24.652 556 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.17 % Favored : 98.64 % 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: 1.66 (0.38), residues: 513 helix: 1.61 (0.28), residues: 370 sheet: None (None), residues: 0 loop : -0.13 (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 0.001 PHE A 204 TYR 0.012 0.001 TYR A 275 ARG 0.003 0.000 ARG A 321 *********************** 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 60 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.380 Fit side-chains REVERT: A 9 ARG cc_start: 0.6479 (ptm160) cc_final: 0.6107 (ttt90) REVERT: A 390 LEU cc_start: 0.7124 (tt) cc_final: 0.6769 (mt) outliers start: 6 outliers final: 6 residues processed: 59 average time/residue: 0.1681 time to fit residues: 12.4167 Evaluate side-chains 60 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 193 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 12 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 26 optimal weight: 0.1980 chunk 27 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 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 = 0.4182 r_free = 0.4182 target = 0.189379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.138769 restraints weight = 4169.782| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.40 r_work: 0.3556 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 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 0.038 4028 Z= 0.185 Angle : 0.589 10.231 5504 Z= 0.286 Chirality : 0.039 0.135 649 Planarity : 0.005 0.043 691 Dihedral : 4.093 26.049 556 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.56 % Favored : 98.25 % Rotamer: Outliers : 1.21 % Allowed : 14.49 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.38), residues: 513 helix: 1.55 (0.28), residues: 370 sheet: None (None), residues: 0 loop : -0.15 (0.52), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 357 HIS 0.002 0.001 HIS A 47 PHE 0.014 0.002 PHE A 204 TYR 0.013 0.001 TYR A 275 ARG 0.004 0.000 ARG A 321 ********************** 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 59 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.410 Fit side-chains REVERT: A 9 ARG cc_start: 0.6694 (ptm160) cc_final: 0.6344 (ttt90) REVERT: A 321 ARG cc_start: 0.7148 (tpp80) cc_final: 0.6891 (ttm-80) REVERT: A 390 LEU cc_start: 0.7126 (tt) cc_final: 0.6743 (mt) outliers start: 5 outliers final: 5 residues processed: 59 average time/residue: 0.1677 time to fit residues: 12.4457 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 : 0.436 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 8.9990 chunk 50 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4191 r_free = 0.4191 target = 0.190412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.139915 restraints weight = 4123.968| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.41 r_work: 0.3567 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4028 Z= 0.174 Angle : 0.584 9.978 5504 Z= 0.283 Chirality : 0.038 0.130 649 Planarity : 0.004 0.042 691 Dihedral : 4.106 27.515 556 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.78 % Favored : 99.03 % 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: 1.57 (0.28), residues: 370 sheet: None (None), residues: 0 loop : -0.15 (0.52), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 357 HIS 0.002 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 321 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2171.96 seconds wall clock time: 37 minutes 53.68 seconds (2273.68 seconds total)