Starting phenix.real_space_refine on Tue Aug 4 17:47:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wrr_37787/08_2026/8wrr_37787.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wrr_37787/08_2026/8wrr_37787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wrr_37787/08_2026/8wrr_37787.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wrr_37787/08_2026/8wrr_37787.map" model { file = "/net/cci-nas-00/data/ceres_data/8wrr_37787/08_2026/8wrr_37787.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wrr_37787/08_2026/8wrr_37787.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 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 P 59 5.49 5 S 9 5.16 5 C 3397 2.51 5 N 1030 2.21 5 O 1189 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5684 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4455 Classifications: {'peptide': 559} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 38, 'TRANS': 520} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 627 Classifications: {'RNA': 30} Modifications used: {'rna2p_pyr': 7, 'rna3p_pur': 10, 'rna3p_pyr': 13} Link IDs: {'rna2p': 7, 'rna3p': 22} Chain: "C" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 379 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "D" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 223 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Time building chain proxies: 1.51, per 1000 atoms: 0.27 Number of scatterers: 5684 At special positions: 0 Unit cell: (89.76, 93.72, 124.74, 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) S 9 16.00 P 59 15.00 O 1189 8.00 N 1030 7.00 C 3397 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 316.4 milliseconds 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1044 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 3 sheets defined 48.7% alpha, 10.2% beta 10 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 75 through 90 removed outlier: 3.761A pdb=" N GLY A 90 " --> pdb=" O GLU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 99 Processing helix chain 'A' and resid 105 through 117 removed outlier: 4.007A pdb=" N ARG A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 169 removed outlier: 4.073A pdb=" N LEU A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ILE A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.698A pdb=" N ILE A 238 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 281 through 291 removed outlier: 3.783A pdb=" N LYS A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 319 Processing helix chain 'A' and resid 327 through 333 Processing helix chain 'A' and resid 367 through 381 removed outlier: 3.759A pdb=" N LYS A 371 " --> pdb=" O GLY A 367 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA A 379 " --> pdb=" O LEU A 375 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 449 removed outlier: 3.911A pdb=" N ALA A 438 " --> pdb=" O ARG A 434 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ALA A 447 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL A 449 " --> pdb=" O ALA A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 469 removed outlier: 4.003A pdb=" N VAL A 459 " --> pdb=" O CYS A 455 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LYS A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N VAL A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN A 464 " --> pdb=" O VAL A 460 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA A 467 " --> pdb=" O ASN A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 500 Processing helix chain 'A' and resid 501 through 503 No H-bonds generated for 'chain 'A' and resid 501 through 503' Processing helix chain 'A' and resid 523 through 527 removed outlier: 3.695A pdb=" N ARG A 526 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS A 527 " --> pdb=" O VAL A 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 523 through 527' Processing helix chain 'A' and resid 530 through 535 Processing helix chain 'A' and resid 542 through 547 removed outlier: 3.593A pdb=" N ALA A 546 " --> pdb=" O GLU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 556 removed outlier: 3.778A pdb=" N ARG A 556 " --> pdb=" O TRP A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 588 removed outlier: 3.615A pdb=" N SER A 565 " --> pdb=" O TYR A 561 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG A 566 " --> pdb=" O VAL A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 637 Processing helix chain 'A' and resid 637 through 642 Processing sheet with id=AA1, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.612A pdb=" N VAL A 340 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP A 342 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE A 347 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASN A 64 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL A 306 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLN A 68 " --> pdb=" O TRP A 304 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TRP A 304 " --> pdb=" O GLN A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 365 through 366 removed outlier: 7.701A pdb=" N VAL A 595 " --> pdb=" O GLY A 385 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL A 387 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 384 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE A 401 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY A 417 " --> pdb=" O PHE A 401 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ARG A 403 " --> pdb=" O PRO A 415 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LYS A 405 " --> pdb=" O ALA A 413 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ALA A 413 " --> pdb=" O LYS A 405 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 513 through 515 removed outlier: 3.801A pdb=" N LYS A 513 " --> pdb=" O GLU A 522 " (cutoff:3.500A) 186 hydrogen bonds defined for protein. 525 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 1.05 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1376 1.33 - 1.45: 1353 1.45 - 1.57: 3070 1.57 - 1.69: 115 1.69 - 1.81: 13 Bond restraints: 5927 Sorted by residual: bond pdb=" N9 G B -20 " pdb=" C4 G B -20 " ideal model delta sigma weight residual 1.375 1.401 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DG D -7 " pdb=" C2' DG D -7 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DT C 3 " pdb=" C2' DT C 3 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.60e+00 bond pdb=" C3' DG D -8 " pdb=" C2' DG D -8 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.72e+00 bond pdb=" N3 G B -20 " pdb=" C4 G B -20 " ideal model delta sigma weight residual 1.350 1.367 -0.017 7.00e-03 2.04e+04 6.21e+00 ... (remaining 5922 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 7882 1.53 - 3.06: 359 3.06 - 4.59: 32 4.59 - 6.13: 6 6.13 - 7.66: 4 Bond angle restraints: 8283 Sorted by residual: angle pdb=" N3 DT C 3 " pdb=" C4 DT C 3 " pdb=" O4 DT C 3 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT D -2 " pdb=" C4 DT D -2 " pdb=" O4 DT D -2 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.66e+01 angle pdb=" N3 DT C 4 " pdb=" C4 DT C 4 " pdb=" O4 DT C 4 " ideal model delta sigma weight residual 119.90 122.31 -2.41 6.00e-01 2.78e+00 1.61e+01 angle pdb=" N3 DT D -9 " pdb=" C4 DT D -9 " pdb=" O4 DT D -9 " ideal model delta sigma weight residual 119.90 122.31 -2.41 6.00e-01 2.78e+00 1.61e+01 angle pdb=" N3 DT C -7 " pdb=" C4 DT C -7 " pdb=" O4 DT C -7 " ideal model delta sigma weight residual 119.90 122.30 -2.40 6.00e-01 2.78e+00 1.60e+01 ... (remaining 8278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 3321 35.66 - 71.32: 250 71.32 - 106.98: 16 106.98 - 142.64: 0 142.64 - 178.30: 3 Dihedral angle restraints: 3590 sinusoidal: 1976 harmonic: 1614 Sorted by residual: dihedral pdb=" O4' U B -9 " pdb=" C1' U B -9 " pdb=" N1 U B -9 " pdb=" C2 U B -9 " ideal model delta sinusoidal sigma weight residual -128.00 48.34 -176.34 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C B -19 " pdb=" C1' C B -19 " pdb=" N1 C B -19 " pdb=" C2 C B -19 " ideal model delta sinusoidal sigma weight residual -128.00 45.88 -173.88 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" C ASN A 151 " pdb=" N ASN A 151 " pdb=" CA ASN A 151 " pdb=" CB ASN A 151 " ideal model delta harmonic sigma weight residual -122.60 -135.97 13.37 0 2.50e+00 1.60e-01 2.86e+01 ... (remaining 3587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 866 0.096 - 0.192: 73 0.192 - 0.288: 0 0.288 - 0.384: 0 0.384 - 0.480: 1 Chirality restraints: 940 Sorted by residual: chirality pdb=" CA ASN A 151 " pdb=" N ASN A 151 " pdb=" C ASN A 151 " pdb=" CB ASN A 151 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.77e+00 chirality pdb=" CA GLU A 440 " pdb=" N GLU A 440 " pdb=" C GLU A 440 " pdb=" CB GLU A 440 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.86e-01 chirality pdb=" CB ILE A 443 " pdb=" CA ILE A 443 " pdb=" CG1 ILE A 443 " pdb=" CG2 ILE A 443 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 937 not shown) Planarity restraints: 852 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 217 " -0.033 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO A 218 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 218 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 218 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 242 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO A 243 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 323 " -0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO A 324 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 324 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 324 " -0.025 5.00e-02 4.00e+02 ... (remaining 849 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1161 2.78 - 3.31: 5186 3.31 - 3.84: 9847 3.84 - 4.37: 11526 4.37 - 4.90: 17718 Nonbonded interactions: 45438 Sorted by model distance: nonbonded pdb=" OG SER A 327 " pdb=" OE1 GLU A 330 " model vdw 2.253 3.040 nonbonded pdb=" O ALA A 268 " pdb=" NH1 ARG A 271 " model vdw 2.273 3.120 nonbonded pdb=" NH2 ARG A 260 " pdb=" OP2 U B -17 " model vdw 2.286 3.120 nonbonded pdb=" OD1 ASP A 428 " pdb=" NH2 ARG A 431 " model vdw 2.301 3.120 nonbonded pdb=" O TRP A 112 " pdb=" OG1 THR A 116 " model vdw 2.313 3.040 ... (remaining 45433 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.000 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.810 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5927 Z= 0.283 Angle : 0.681 7.656 8283 Z= 0.481 Chirality : 0.051 0.480 940 Planarity : 0.006 0.051 852 Dihedral : 20.701 178.297 2546 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.31 % Allowed : 0.84 % Favored : 96.85 % Cbeta Deviations : 0.19 % 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 are not related in a simple way. whole: -0.53 (0.36), residues: 553 helix: 0.16 (0.35), residues: 231 sheet: -0.72 (0.72), residues: 57 loop : -0.62 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 271 TYR 0.008 0.001 TYR A 317 PHE 0.015 0.001 PHE A 635 TRP 0.026 0.001 TRP A 318 HIS 0.001 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.28 ( 5927) covalent geometry : angle 0.68077 / 0.48 ( 8283) hydrogen bonds : bond 0.18286 / 12.94 ( 211) hydrogen bonds : angle 7.71826 / 5.43 ( 575) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.113 Fit side-chains REVERT: A 110 ASP cc_start: 0.6976 (p0) cc_final: 0.6735 (p0) REVERT: A 151 ASN cc_start: 0.6334 (OUTLIER) cc_final: 0.5953 (p0) REVERT: A 514 SER cc_start: 0.6885 (OUTLIER) cc_final: 0.6235 (t) outliers start: 11 outliers final: 3 residues processed: 90 average time/residue: 0.1063 time to fit residues: 11.4787 Evaluate side-chains 82 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 154 ARG Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 514 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN A 383 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.157454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.121574 restraints weight = 8197.300| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.71 r_work: 0.3311 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 5927 Z= 0.248 Angle : 0.696 11.924 8283 Z= 0.372 Chirality : 0.049 0.218 940 Planarity : 0.007 0.056 852 Dihedral : 23.061 177.754 1420 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.89 % Allowed : 9.45 % Favored : 88.66 % 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 are not related in a simple way. whole: -0.76 (0.35), residues: 553 helix: -0.01 (0.34), residues: 230 sheet: -0.91 (0.66), residues: 57 loop : -0.74 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 585 TYR 0.012 0.002 TYR A 245 PHE 0.010 0.002 PHE A 113 TRP 0.021 0.002 TRP A 318 HIS 0.004 0.001 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.25 ( 5927) covalent geometry : angle 0.69582 / 0.37 ( 8283) hydrogen bonds : bond 0.07088 / 5.25 ( 211) hydrogen bonds : angle 5.30414 / 3.72 ( 575) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.124 Fit side-chains revert: symmetry clash REVERT: A 110 ASP cc_start: 0.7667 (p0) cc_final: 0.7394 (p0) REVERT: A 403 ARG cc_start: 0.8237 (mtm180) cc_final: 0.7988 (mtm180) REVERT: A 514 SER cc_start: 0.6500 (OUTLIER) cc_final: 0.6098 (t) REVERT: A 560 GLU cc_start: 0.6509 (mp0) cc_final: 0.6281 (mp0) outliers start: 9 outliers final: 5 residues processed: 94 average time/residue: 0.1135 time to fit residues: 12.6112 Evaluate side-chains 92 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 154 ARG Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 514 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 47 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 0.0980 chunk 30 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 5 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN A 127 GLN A 203 GLN A 383 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.158049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.122893 restraints weight = 8167.872| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.71 r_work: 0.3350 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5927 Z= 0.172 Angle : 0.604 10.104 8283 Z= 0.329 Chirality : 0.044 0.195 940 Planarity : 0.006 0.053 852 Dihedral : 23.232 177.351 1418 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.15 % Allowed : 10.92 % Favored : 85.92 % 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 are not related in a simple way. whole: -0.65 (0.35), residues: 553 helix: -0.01 (0.34), residues: 231 sheet: -0.58 (0.64), residues: 55 loop : -0.66 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 585 TYR 0.011 0.001 TYR A 432 PHE 0.008 0.001 PHE A 102 TRP 0.019 0.001 TRP A 318 HIS 0.003 0.001 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 ( 5927) covalent geometry : angle 0.60381 / 0.33 ( 8283) hydrogen bonds : bond 0.05794 / 4.20 ( 211) hydrogen bonds : angle 4.98282 / 3.51 ( 575) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 403 ARG cc_start: 0.8156 (mtm180) cc_final: 0.7926 (mtm180) REVERT: A 431 ARG cc_start: 0.7564 (mtm110) cc_final: 0.7104 (mtm180) REVERT: A 514 SER cc_start: 0.6408 (OUTLIER) cc_final: 0.5967 (t) REVERT: A 560 GLU cc_start: 0.6484 (mp0) cc_final: 0.6250 (mp0) outliers start: 15 outliers final: 7 residues processed: 95 average time/residue: 0.1221 time to fit residues: 14.0133 Evaluate side-chains 89 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 595 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 1 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 0.0670 chunk 16 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 GLN A 383 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.157273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.122076 restraints weight = 8182.605| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.70 r_work: 0.3343 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5927 Z= 0.186 Angle : 0.603 9.599 8283 Z= 0.329 Chirality : 0.044 0.206 940 Planarity : 0.006 0.053 852 Dihedral : 23.186 177.491 1414 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.94 % Allowed : 13.24 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.35), residues: 553 helix: 0.04 (0.34), residues: 231 sheet: -0.65 (0.62), residues: 55 loop : -0.77 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 585 TYR 0.011 0.002 TYR A 245 PHE 0.008 0.001 PHE A 102 TRP 0.021 0.001 TRP A 318 HIS 0.003 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.19 ( 5927) covalent geometry : angle 0.60286 / 0.33 ( 8283) hydrogen bonds : bond 0.05556 / 4.05 ( 211) hydrogen bonds : angle 4.84783 / 3.40 ( 575) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 LEU cc_start: 0.8856 (mt) cc_final: 0.8550 (mp) REVERT: A 431 ARG cc_start: 0.7561 (mtm110) cc_final: 0.7065 (mtm180) REVERT: A 514 SER cc_start: 0.6520 (OUTLIER) cc_final: 0.6099 (t) REVERT: A 560 GLU cc_start: 0.6497 (mp0) cc_final: 0.6262 (mp0) outliers start: 14 outliers final: 11 residues processed: 89 average time/residue: 0.1146 time to fit residues: 12.4611 Evaluate side-chains 90 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 595 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 42 optimal weight: 7.9990 chunk 18 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN A 383 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.156452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.120757 restraints weight = 8222.764| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.70 r_work: 0.3344 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5927 Z= 0.229 Angle : 0.635 9.778 8283 Z= 0.343 Chirality : 0.047 0.203 940 Planarity : 0.006 0.054 852 Dihedral : 23.232 177.328 1414 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.15 % Allowed : 13.66 % Favored : 83.19 % 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 are not related in a simple way. whole: -0.74 (0.35), residues: 553 helix: 0.05 (0.33), residues: 231 sheet: -0.63 (0.59), residues: 65 loop : -0.86 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 585 TYR 0.014 0.002 TYR A 201 PHE 0.009 0.001 PHE A 102 TRP 0.023 0.002 TRP A 318 HIS 0.005 0.001 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.23 ( 5927) covalent geometry : angle 0.63476 / 0.34 ( 8283) hydrogen bonds : bond 0.05681 / 4.10 ( 211) hydrogen bonds : angle 4.87060 / 3.41 ( 575) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 72 LEU cc_start: 0.8863 (mt) cc_final: 0.8554 (mp) REVERT: A 110 ASP cc_start: 0.7691 (p0) cc_final: 0.7416 (p0) REVERT: A 431 ARG cc_start: 0.7630 (mtm110) cc_final: 0.7083 (mtm180) REVERT: A 514 SER cc_start: 0.6718 (OUTLIER) cc_final: 0.6351 (t) REVERT: A 560 GLU cc_start: 0.6536 (mp0) cc_final: 0.6313 (mp0) outliers start: 15 outliers final: 9 residues processed: 88 average time/residue: 0.1118 time to fit residues: 12.0364 Evaluate side-chains 86 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 595 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 0.0970 chunk 12 optimal weight: 0.4980 chunk 35 optimal weight: 0.0980 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 0.0980 chunk 39 optimal weight: 0.0970 chunk 52 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.1776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.159333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.124225 restraints weight = 8135.563| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.68 r_work: 0.3346 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5927 Z= 0.121 Angle : 0.554 9.708 8283 Z= 0.305 Chirality : 0.042 0.206 940 Planarity : 0.006 0.052 852 Dihedral : 23.238 178.760 1410 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.36 % Allowed : 13.24 % Favored : 83.40 % 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 are not related in a simple way. whole: -0.33 (0.35), residues: 553 helix: 0.39 (0.34), residues: 230 sheet: -0.20 (0.62), residues: 65 loop : -0.69 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 585 TYR 0.010 0.001 TYR A 432 PHE 0.007 0.001 PHE A 102 TRP 0.027 0.001 TRP A 318 HIS 0.002 0.000 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 ( 5927) covalent geometry : angle 0.55413 / 0.30 ( 8283) hydrogen bonds : bond 0.04743 / 3.43 ( 211) hydrogen bonds : angle 4.59645 / 3.22 ( 575) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 157 LYS cc_start: 0.6703 (OUTLIER) cc_final: 0.6327 (mttp) REVERT: A 431 ARG cc_start: 0.7594 (mtm110) cc_final: 0.7092 (mtm180) REVERT: A 446 GLU cc_start: 0.5715 (OUTLIER) cc_final: 0.5423 (pm20) REVERT: A 560 GLU cc_start: 0.6524 (mp0) cc_final: 0.6294 (mp0) outliers start: 16 outliers final: 10 residues processed: 90 average time/residue: 0.1126 time to fit residues: 12.4208 Evaluate side-chains 89 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 633 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 31 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 49 optimal weight: 0.3980 chunk 42 optimal weight: 3.9990 chunk 19 optimal weight: 0.0040 chunk 46 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.158007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.122420 restraints weight = 8223.703| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.70 r_work: 0.3368 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5927 Z= 0.174 Angle : 0.617 20.870 8283 Z= 0.319 Chirality : 0.044 0.206 940 Planarity : 0.006 0.052 852 Dihedral : 23.168 177.582 1409 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.15 % Allowed : 14.71 % Favored : 82.14 % 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 are not related in a simple way. whole: -0.36 (0.35), residues: 553 helix: 0.40 (0.34), residues: 230 sheet: -0.35 (0.62), residues: 65 loop : -0.71 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 585 TYR 0.011 0.002 TYR A 432 PHE 0.008 0.001 PHE A 102 TRP 0.024 0.001 TRP A 318 HIS 0.003 0.001 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 ( 5927) covalent geometry : angle 0.61712 / 0.32 ( 8283) hydrogen bonds : bond 0.05004 / 3.61 ( 211) hydrogen bonds : angle 4.60094 / 3.21 ( 575) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: A 72 LEU cc_start: 0.8865 (mt) cc_final: 0.8565 (mp) REVERT: A 157 LYS cc_start: 0.6678 (OUTLIER) cc_final: 0.6294 (mttp) REVERT: A 431 ARG cc_start: 0.7634 (mtm110) cc_final: 0.7113 (mtm180) REVERT: A 560 GLU cc_start: 0.6557 (mp0) cc_final: 0.6316 (mp0) outliers start: 15 outliers final: 11 residues processed: 89 average time/residue: 0.1014 time to fit residues: 11.1204 Evaluate side-chains 90 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 595 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 27 optimal weight: 0.7980 chunk 25 optimal weight: 0.3980 chunk 58 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 39 optimal weight: 0.0570 chunk 9 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 1 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN A 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.158753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.123542 restraints weight = 8142.390| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.68 r_work: 0.3335 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5927 Z= 0.148 Angle : 0.590 18.216 8283 Z= 0.309 Chirality : 0.043 0.207 940 Planarity : 0.006 0.053 852 Dihedral : 23.201 178.059 1409 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.99 % Allowed : 13.45 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.36), residues: 553 helix: 0.53 (0.34), residues: 230 sheet: -0.24 (0.62), residues: 65 loop : -0.66 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 585 TYR 0.018 0.002 TYR A 209 PHE 0.008 0.001 PHE A 102 TRP 0.027 0.001 TRP A 318 HIS 0.003 0.001 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 ( 5927) covalent geometry : angle 0.59039 / 0.31 ( 8283) hydrogen bonds : bond 0.04701 / 3.38 ( 211) hydrogen bonds : angle 4.52630 / 3.17 ( 575) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: A 72 LEU cc_start: 0.8822 (mt) cc_final: 0.8532 (mp) REVERT: A 157 LYS cc_start: 0.6703 (OUTLIER) cc_final: 0.6333 (mttp) REVERT: A 431 ARG cc_start: 0.7612 (mtm110) cc_final: 0.7082 (mtm180) REVERT: A 446 GLU cc_start: 0.5723 (OUTLIER) cc_final: 0.5413 (pm20) REVERT: A 560 GLU cc_start: 0.6546 (mp0) cc_final: 0.6295 (mp0) outliers start: 19 outliers final: 13 residues processed: 93 average time/residue: 0.1131 time to fit residues: 12.9003 Evaluate side-chains 93 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 633 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 6 optimal weight: 0.2980 chunk 8 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 42 optimal weight: 0.0370 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN A 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.158723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.123441 restraints weight = 8067.023| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.67 r_work: 0.3365 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5927 Z= 0.165 Angle : 0.603 18.022 8283 Z= 0.316 Chirality : 0.043 0.207 940 Planarity : 0.006 0.052 852 Dihedral : 23.190 177.477 1409 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.57 % Allowed : 14.08 % Favored : 82.35 % 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 are not related in a simple way. whole: -0.24 (0.36), residues: 553 helix: 0.53 (0.34), residues: 230 sheet: -0.32 (0.62), residues: 65 loop : -0.67 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 585 TYR 0.016 0.002 TYR A 209 PHE 0.008 0.001 PHE A 102 TRP 0.027 0.001 TRP A 318 HIS 0.003 0.001 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 ( 5927) covalent geometry : angle 0.60336 / 0.32 ( 8283) hydrogen bonds : bond 0.04790 / 3.43 ( 211) hydrogen bonds : angle 4.50590 / 3.15 ( 575) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.109 Fit side-chains revert: symmetry clash REVERT: A 72 LEU cc_start: 0.8864 (mt) cc_final: 0.8549 (mp) REVERT: A 157 LYS cc_start: 0.6689 (OUTLIER) cc_final: 0.6337 (mttp) REVERT: A 431 ARG cc_start: 0.7634 (mtm110) cc_final: 0.7111 (mtm180) REVERT: A 446 GLU cc_start: 0.5703 (OUTLIER) cc_final: 0.5395 (pm20) REVERT: A 560 GLU cc_start: 0.6548 (mp0) cc_final: 0.6305 (mp0) outliers start: 17 outliers final: 13 residues processed: 91 average time/residue: 0.0914 time to fit residues: 10.3030 Evaluate side-chains 96 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 633 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 57 optimal weight: 2.9990 chunk 25 optimal weight: 0.0970 chunk 29 optimal weight: 0.1980 chunk 27 optimal weight: 0.8980 chunk 5 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN A 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.159367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.124263 restraints weight = 8205.289| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.69 r_work: 0.3388 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5927 Z= 0.139 Angle : 0.582 16.913 8283 Z= 0.307 Chirality : 0.042 0.208 940 Planarity : 0.006 0.053 852 Dihedral : 23.208 177.882 1409 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.15 % Allowed : 14.50 % Favored : 82.35 % 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 are not related in a simple way. whole: -0.10 (0.36), residues: 553 helix: 0.65 (0.35), residues: 230 sheet: -0.19 (0.63), residues: 65 loop : -0.61 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 585 TYR 0.016 0.002 TYR A 209 PHE 0.007 0.001 PHE A 102 TRP 0.029 0.001 TRP A 318 HIS 0.002 0.001 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 ( 5927) covalent geometry : angle 0.58225 / 0.31 ( 8283) hydrogen bonds : bond 0.04485 / 3.20 ( 211) hydrogen bonds : angle 4.42984 / 3.09 ( 575) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: A 72 LEU cc_start: 0.8857 (mt) cc_final: 0.8545 (mp) REVERT: A 157 LYS cc_start: 0.6686 (OUTLIER) cc_final: 0.6350 (mttp) REVERT: A 431 ARG cc_start: 0.7622 (mtm110) cc_final: 0.7112 (mtm180) REVERT: A 446 GLU cc_start: 0.5739 (OUTLIER) cc_final: 0.5429 (pm20) REVERT: A 560 GLU cc_start: 0.6536 (mp0) cc_final: 0.6297 (mp0) outliers start: 15 outliers final: 11 residues processed: 90 average time/residue: 0.1061 time to fit residues: 11.9597 Evaluate side-chains 94 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 633 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 55 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 34 optimal weight: 0.0980 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN A 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.158240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.122802 restraints weight = 8071.600| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.67 r_work: 0.3363 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5927 Z= 0.194 Angle : 0.629 16.749 8283 Z= 0.328 Chirality : 0.045 0.207 940 Planarity : 0.006 0.052 852 Dihedral : 23.191 177.089 1409 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.36 % Allowed : 14.92 % Favored : 81.72 % 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 are not related in a simple way. whole: -0.27 (0.36), residues: 553 helix: 0.56 (0.35), residues: 230 sheet: -0.55 (0.60), residues: 65 loop : -0.67 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 585 TYR 0.015 0.002 TYR A 209 PHE 0.009 0.001 PHE A 102 TRP 0.025 0.001 TRP A 318 HIS 0.004 0.001 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 ( 5927) covalent geometry : angle 0.62872 / 0.33 ( 8283) hydrogen bonds : bond 0.04923 / 3.52 ( 211) hydrogen bonds : angle 4.50270 / 3.13 ( 575) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1951.90 seconds wall clock time: 33 minutes 58.68 seconds (2038.68 seconds total)