Starting phenix.real_space_refine on Wed Sep 17 04:15:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j5w_61155/09_2025/9j5w_61155.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j5w_61155/09_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_61155/09_2025/9j5w_61155.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j5w_61155/09_2025/9j5w_61155.map" model { file = "/net/cci-nas-00/data/ceres_data/9j5w_61155/09_2025/9j5w_61155.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j5w_61155/09_2025/9j5w_61155.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 3, 'GLU:plan': 1} 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: 1.18, per 1000 atoms: 0.30 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: 0.38 Conformation dependent library (CDL) restraints added in 157.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.09 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: 0.50 Time building geometry restraints manager: 0.51 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: 1.110 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: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.340 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.760 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.004 0.000 ARG A 321 TYR 0.009 0.001 TYR A 275 PHE 0.016 0.001 PHE A 204 TRP 0.010 0.001 TRP A 278 HIS 0.004 0.001 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00805 ( 4028) covalent geometry : angle 0.62172 ( 5504) SS BOND : bond 0.00137 ( 2) SS BOND : angle 0.78315 ( 4) hydrogen bonds : bond 0.20592 ( 251) hydrogen bonds : angle 6.03910 ( 735) *********************** 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 : 0.149 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: 0.0845 time to fit residues: 5.8441 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 : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.0770 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.0470 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 overall best weight: 0.4236 ------------------------------------------------------------------------------- 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 = 0.4269 r_free = 0.4269 target = 0.198544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.146777 restraints weight = 4235.759| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.48 r_work: 0.3644 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.1114 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= 0.132 Angle : 0.586 8.939 5508 Z= 0.287 Chirality : 0.039 0.124 649 Planarity : 0.005 0.043 691 Dihedral : 4.066 22.920 556 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.39 % Favored : 99.42 % Rotamer: Outliers : 0.48 % Allowed : 5.56 % Favored : 93.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.36), residues: 513 helix: 1.48 (0.26), residues: 365 sheet: None (None), residues: 0 loop : -0.14 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 145 TYR 0.010 0.001 TYR A 275 PHE 0.015 0.001 PHE A 204 TRP 0.009 0.001 TRP A 258 HIS 0.002 0.001 HIS A 124 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 4028) covalent geometry : angle 0.58618 ( 5504) SS BOND : bond 0.00247 ( 2) SS BOND : angle 0.76175 ( 4) hydrogen bonds : bond 0.05270 ( 251) hydrogen bonds : angle 4.46111 ( 735) *********************** 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 : 0.148 Fit side-chains REVERT: A 39 ASN cc_start: 0.8376 (t0) cc_final: 0.8173 (m-40) REVERT: A 389 ASP cc_start: 0.7192 (t70) cc_final: 0.6992 (t0) outliers start: 2 outliers final: 1 residues processed: 60 average time/residue: 0.0724 time to fit residues: 5.5037 Evaluate side-chains 49 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.141 ------------------------------------------------------------------------------- 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 18 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.4217 r_free = 0.4217 target = 0.191601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.141760 restraints weight = 4262.505| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.39 r_work: 0.3556 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4030 Z= 0.165 Angle : 0.628 7.454 5508 Z= 0.311 Chirality : 0.042 0.159 649 Planarity : 0.005 0.049 691 Dihedral : 4.164 16.530 556 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.17 % Favored : 98.64 % Rotamer: Outliers : 0.97 % Allowed : 10.63 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.36), residues: 513 helix: 1.30 (0.27), residues: 366 sheet: None (None), residues: 0 loop : -0.29 (0.49), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 145 TYR 0.016 0.002 TYR A 275 PHE 0.016 0.002 PHE A 202 TRP 0.013 0.002 TRP A 258 HIS 0.004 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 4028) covalent geometry : angle 0.62728 ( 5504) SS BOND : bond 0.00459 ( 2) SS BOND : angle 1.03136 ( 4) hydrogen bonds : bond 0.06368 ( 251) hydrogen bonds : angle 4.48207 ( 735) *********************** 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 58 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.123 Fit side-chains REVERT: A 89 LEU cc_start: 0.8438 (mt) cc_final: 0.8002 (mt) outliers start: 4 outliers final: 4 residues processed: 58 average time/residue: 0.0811 time to fit residues: 5.7742 Evaluate side-chains 52 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 388 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 34 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.4184 r_free = 0.4184 target = 0.188692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.138672 restraints weight = 4209.780| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.38 r_work: 0.3539 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4030 Z= 0.161 Angle : 0.604 9.389 5508 Z= 0.299 Chirality : 0.040 0.149 649 Planarity : 0.005 0.046 691 Dihedral : 4.204 19.555 556 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.78 % Favored : 99.03 % Rotamer: Outliers : 1.21 % Allowed : 11.84 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.37), residues: 513 helix: 1.29 (0.27), residues: 366 sheet: None (None), residues: 0 loop : -0.28 (0.50), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 145 TYR 0.015 0.001 TYR A 275 PHE 0.016 0.002 PHE A 204 TRP 0.011 0.001 TRP A 258 HIS 0.003 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 4028) covalent geometry : angle 0.60403 ( 5504) SS BOND : bond 0.00330 ( 2) SS BOND : angle 0.91143 ( 4) hydrogen bonds : bond 0.05888 ( 251) hydrogen bonds : angle 4.39013 ( 735) *********************** 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 60 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.143 Fit side-chains REVERT: A 9 ARG cc_start: 0.6448 (ptm160) cc_final: 0.6107 (ttt90) REVERT: A 390 LEU cc_start: 0.7050 (tt) cc_final: 0.6668 (mt) REVERT: A 434 ARG cc_start: 0.8242 (mmm-85) cc_final: 0.7673 (mmm-85) outliers start: 5 outliers final: 4 residues processed: 60 average time/residue: 0.0776 time to fit residues: 5.8164 Evaluate side-chains 53 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.161 ------------------------------------------------------------------------------- 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 41 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 chunk 7 optimal weight: 0.0770 chunk 4 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 = 0.4192 r_free = 0.4192 target = 0.190312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.139820 restraints weight = 4154.216| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.41 r_work: 0.3552 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4030 Z= 0.126 Angle : 0.579 10.574 5508 Z= 0.282 Chirality : 0.038 0.136 649 Planarity : 0.004 0.044 691 Dihedral : 4.124 20.554 556 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.92 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.37), residues: 513 helix: 1.50 (0.27), residues: 366 sheet: None (None), residues: 0 loop : -0.19 (0.50), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 145 TYR 0.012 0.001 TYR A 275 PHE 0.017 0.001 PHE A 204 TRP 0.012 0.001 TRP A 357 HIS 0.003 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 4028) covalent geometry : angle 0.57841 ( 5504) SS BOND : bond 0.00071 ( 2) SS BOND : angle 0.76500 ( 4) hydrogen bonds : bond 0.05137 ( 251) hydrogen bonds : angle 4.22585 ( 735) *********************** 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 63 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.141 Fit side-chains revert: symmetry clash REVERT: A 9 ARG cc_start: 0.6399 (ptm160) cc_final: 0.6062 (ttt90) REVERT: A 89 LEU cc_start: 0.8430 (mt) cc_final: 0.8035 (mt) REVERT: A 390 LEU cc_start: 0.7049 (tt) cc_final: 0.6653 (mt) REVERT: A 434 ARG cc_start: 0.8189 (mmm-85) cc_final: 0.7652 (mmm-85) outliers start: 2 outliers final: 2 residues processed: 63 average time/residue: 0.0788 time to fit residues: 6.1632 Evaluate side-chains 59 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.143 ------------------------------------------------------------------------------- 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 36 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.4208 r_free = 0.4208 target = 0.190761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.139946 restraints weight = 4268.550| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.42 r_work: 0.3544 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4030 Z= 0.151 Angle : 0.602 9.145 5508 Z= 0.296 Chirality : 0.040 0.147 649 Planarity : 0.005 0.046 691 Dihedral : 4.173 22.738 556 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.97 % Favored : 98.83 % Rotamer: Outliers : 1.69 % Allowed : 12.56 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.37), residues: 513 helix: 1.37 (0.28), residues: 367 sheet: None (None), residues: 0 loop : -0.24 (0.50), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 145 TYR 0.014 0.002 TYR A 275 PHE 0.015 0.002 PHE A 202 TRP 0.018 0.001 TRP A 357 HIS 0.003 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 4028) covalent geometry : angle 0.60151 ( 5504) SS BOND : bond 0.00294 ( 2) SS BOND : angle 0.96254 ( 4) hydrogen bonds : bond 0.05782 ( 251) hydrogen bonds : angle 4.30917 ( 735) *********************** 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 60 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.145 Fit side-chains REVERT: A 9 ARG cc_start: 0.6728 (ptm160) cc_final: 0.6442 (ttt90) REVERT: A 390 LEU cc_start: 0.7190 (tt) cc_final: 0.6710 (mt) outliers start: 7 outliers final: 6 residues processed: 60 average time/residue: 0.0701 time to fit residues: 5.2945 Evaluate side-chains 52 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 SER 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 12 optimal weight: 0.2980 chunk 42 optimal weight: 0.0000 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 overall best weight: 0.5184 ------------------------------------------------------------------------------- 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 = 0.4217 r_free = 0.4217 target = 0.191880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.141687 restraints weight = 4257.896| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.40 r_work: 0.3591 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4030 Z= 0.120 Angle : 0.569 8.616 5508 Z= 0.277 Chirality : 0.038 0.128 649 Planarity : 0.004 0.043 691 Dihedral : 4.109 23.279 556 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.97 % Favored : 98.83 % Rotamer: Outliers : 1.45 % Allowed : 13.53 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.37), residues: 513 helix: 1.50 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -0.18 (0.51), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 321 TYR 0.011 0.001 TYR A 275 PHE 0.017 0.001 PHE A 204 TRP 0.016 0.001 TRP A 357 HIS 0.003 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 4028) covalent geometry : angle 0.56823 ( 5504) SS BOND : bond 0.00514 ( 2) SS BOND : angle 1.47417 ( 4) hydrogen bonds : bond 0.04886 ( 251) hydrogen bonds : angle 4.15762 ( 735) *********************** 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 59 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.148 Fit side-chains REVERT: A 9 ARG cc_start: 0.6783 (ptm160) cc_final: 0.6466 (ttt90) REVERT: A 89 LEU cc_start: 0.8694 (mt) cc_final: 0.8413 (mt) REVERT: A 390 LEU cc_start: 0.7197 (tt) cc_final: 0.6721 (mt) outliers start: 6 outliers final: 6 residues processed: 58 average time/residue: 0.0797 time to fit residues: 5.7962 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 : 0.144 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 6 optimal weight: 0.0770 chunk 46 optimal weight: 0.5980 chunk 31 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 19 optimal weight: 0.0970 chunk 43 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 = 0.4216 r_free = 0.4216 target = 0.191682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.142143 restraints weight = 4146.505| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.35 r_work: 0.3592 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4030 Z= 0.120 Angle : 0.567 7.964 5508 Z= 0.276 Chirality : 0.038 0.129 649 Planarity : 0.004 0.044 691 Dihedral : 4.061 25.044 556 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.36 % Favored : 98.44 % Rotamer: Outliers : 1.93 % Allowed : 13.53 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.38), residues: 513 helix: 1.51 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -0.18 (0.53), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 321 TYR 0.012 0.001 TYR A 275 PHE 0.016 0.001 PHE A 204 TRP 0.021 0.001 TRP A 357 HIS 0.002 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 4028) covalent geometry : angle 0.56563 ( 5504) SS BOND : bond 0.00294 ( 2) SS BOND : angle 1.60032 ( 4) hydrogen bonds : bond 0.04795 ( 251) hydrogen bonds : angle 4.10124 ( 735) *********************** 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 59 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.126 Fit side-chains REVERT: A 9 ARG cc_start: 0.6859 (ptm160) cc_final: 0.6489 (ttt90) REVERT: A 321 ARG cc_start: 0.6897 (tpp80) cc_final: 0.6644 (ttm-80) REVERT: A 390 LEU cc_start: 0.7220 (tt) cc_final: 0.6688 (mt) outliers start: 8 outliers final: 8 residues processed: 58 average time/residue: 0.0650 time to fit residues: 4.7407 Evaluate side-chains 59 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 125 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 33 optimal weight: 5.9990 chunk 11 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4207 r_free = 0.4207 target = 0.190607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.140513 restraints weight = 4212.711| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.39 r_work: 0.3581 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.3021 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 : 0.569 7.783 5508 Z= 0.277 Chirality : 0.038 0.133 649 Planarity : 0.005 0.044 691 Dihedral : 4.105 26.942 556 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.36 % Favored : 98.44 % Rotamer: Outliers : 1.93 % Allowed : 13.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.38), residues: 513 helix: 1.49 (0.28), residues: 370 sheet: None (None), residues: 0 loop : -0.18 (0.52), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 321 TYR 0.013 0.001 TYR A 275 PHE 0.016 0.001 PHE A 204 TRP 0.019 0.001 TRP A 357 HIS 0.002 0.000 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 4028) covalent geometry : angle 0.56839 ( 5504) SS BOND : bond 0.00357 ( 2) SS BOND : angle 1.43048 ( 4) hydrogen bonds : bond 0.05044 ( 251) hydrogen bonds : angle 4.14219 ( 735) *********************** 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: 8 poor density : 52 time to evaluate : 0.152 Fit side-chains REVERT: A 9 ARG cc_start: 0.6931 (ptm160) cc_final: 0.6598 (ttt90) REVERT: A 321 ARG cc_start: 0.7066 (tpp80) cc_final: 0.6819 (ttm-80) REVERT: A 390 LEU cc_start: 0.7176 (tt) cc_final: 0.6741 (mt) outliers start: 8 outliers final: 8 residues processed: 59 average time/residue: 0.0742 time to fit residues: 5.4501 Evaluate side-chains 60 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 125 SER 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 9 optimal weight: 5.9990 chunk 39 optimal weight: 0.0000 chunk 30 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 42 optimal weight: 0.0070 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 50 optimal weight: 0.0770 chunk 40 optimal weight: 0.6980 overall best weight: 0.2960 ------------------------------------------------------------------------------- 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 = 0.4237 r_free = 0.4237 target = 0.194214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.144612 restraints weight = 4134.648| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.38 r_work: 0.3619 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4030 Z= 0.111 Angle : 0.549 7.831 5508 Z= 0.267 Chirality : 0.037 0.119 649 Planarity : 0.004 0.043 691 Dihedral : 4.040 27.575 556 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.97 % Favored : 98.83 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.38), residues: 513 helix: 1.62 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -0.18 (0.53), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 321 TYR 0.011 0.001 TYR A 275 PHE 0.019 0.001 PHE A 204 TRP 0.020 0.001 TRP A 357 HIS 0.002 0.000 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 4028) covalent geometry : angle 0.54791 ( 5504) SS BOND : bond 0.00208 ( 2) SS BOND : angle 1.38650 ( 4) hydrogen bonds : bond 0.04221 ( 251) hydrogen bonds : angle 4.00829 ( 735) ********************** 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 58 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.126 Fit side-chains REVERT: A 117 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7001 (mm-30) REVERT: A 321 ARG cc_start: 0.7032 (tpp80) cc_final: 0.6807 (ttm-80) REVERT: A 390 LEU cc_start: 0.7158 (tt) cc_final: 0.6750 (mt) outliers start: 6 outliers final: 5 residues processed: 57 average time/residue: 0.0782 time to fit residues: 5.5417 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 : 0.160 ------------------------------------------------------------------------------- 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 250 SER Chi-restraints excluded: chain A residue 403 LEU 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 16 optimal weight: 4.9990 chunk 2 optimal weight: 0.0470 chunk 46 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 chunk 45 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 overall best weight: 0.4678 ------------------------------------------------------------------------------- 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 = 0.4230 r_free = 0.4230 target = 0.192877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.143830 restraints weight = 4098.449| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.33 r_work: 0.3617 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4030 Z= 0.114 Angle : 0.545 7.606 5508 Z= 0.264 Chirality : 0.037 0.124 649 Planarity : 0.004 0.044 691 Dihedral : 4.026 28.444 556 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.36 % Favored : 98.44 % Rotamer: Outliers : 1.21 % Allowed : 14.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.38), residues: 513 helix: 1.62 (0.28), residues: 370 sheet: None (None), residues: 0 loop : -0.15 (0.53), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 321 TYR 0.013 0.002 TYR A 253 PHE 0.017 0.001 PHE A 204 TRP 0.017 0.001 TRP A 357 HIS 0.002 0.000 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 4028) covalent geometry : angle 0.54364 ( 5504) SS BOND : bond 0.00263 ( 2) SS BOND : angle 1.29164 ( 4) hydrogen bonds : bond 0.04462 ( 251) hydrogen bonds : angle 4.00607 ( 735) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1212.95 seconds wall clock time: 21 minutes 26.71 seconds (1286.71 seconds total)