Starting phenix.real_space_refine on Sat May 10 08:14:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wrr_37787/05_2025/8wrr_37787.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wrr_37787/05_2025/8wrr_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_37787/05_2025/8wrr_37787.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wrr_37787/05_2025/8wrr_37787.map" model { file = "/net/cci-nas-00/data/ceres_data/8wrr_37787/05_2025/8wrr_37787.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wrr_37787/05_2025/8wrr_37787.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.41, per 1000 atoms: 0.78 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: 1.53 Conformation dependent library (CDL) restraints added in 653.3 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: 2.00 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: 1.87 Time building geometry restraints manager: 1.77 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=" CA ASN A 151 " pdb=" CB ASN A 151 " ideal model delta sigma weight residual 1.528 1.552 -0.024 1.56e-02 4.11e+03 2.31e+00 bond pdb=" CA THR A 521 " pdb=" CB THR A 521 " ideal model delta sigma weight residual 1.523 1.539 -0.016 1.21e-02 6.83e+03 1.80e+00 bond pdb=" N9 G B -20 " pdb=" C4 G B -20 " ideal model delta sigma weight residual 1.375 1.401 -0.026 2.00e-02 2.50e+03 1.74e+00 bond pdb=" C GLU A 148 " pdb=" O GLU A 148 " ideal model delta sigma weight residual 1.236 1.222 0.014 1.15e-02 7.56e+03 1.54e+00 bond pdb=" CA ARG A 155 " pdb=" C ARG A 155 " ideal model delta sigma weight residual 1.524 1.508 0.016 1.27e-02 6.20e+03 1.50e+00 ... (remaining 5922 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 8013 1.53 - 3.06: 227 3.06 - 4.59: 33 4.59 - 6.13: 6 6.13 - 7.66: 4 Bond angle restraints: 8283 Sorted by residual: angle pdb=" C ASP A 528 " pdb=" N TYR A 529 " pdb=" CA TYR A 529 " ideal model delta sigma weight residual 121.54 128.55 -7.01 1.91e+00 2.74e-01 1.35e+01 angle pdb=" C ASN A 151 " pdb=" CA ASN A 151 " pdb=" CB ASN A 151 " ideal model delta sigma weight residual 110.79 116.39 -5.60 1.66e+00 3.63e-01 1.14e+01 angle pdb=" C PRO A 484 " pdb=" N TRP A 485 " pdb=" CA TRP A 485 " ideal model delta sigma weight residual 121.54 127.78 -6.24 1.91e+00 2.74e-01 1.07e+01 angle pdb=" N ASN A 195 " pdb=" CA ASN A 195 " pdb=" C ASN A 195 " ideal model delta sigma weight residual 110.07 114.09 -4.02 1.26e+00 6.30e-01 1.02e+01 angle pdb=" N LYS A 146 " pdb=" CA LYS A 146 " pdb=" C LYS A 146 " ideal model delta sigma weight residual 111.07 107.75 3.32 1.07e+00 8.73e-01 9.61e+00 ... (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: 896 0.096 - 0.192: 43 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: 3.340 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.720 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5927 Z= 0.162 Angle : 0.608 7.656 8283 Z= 0.346 Chirality : 0.043 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.026 0.001 TRP A 318 HIS 0.001 0.001 HIS A 253 PHE 0.015 0.001 PHE A 635 TYR 0.008 0.001 TYR A 317 ARG 0.007 0.000 ARG A 271 Details of bonding type rmsd hydrogen bonds : bond 0.18286 ( 211) hydrogen bonds : angle 7.71826 ( 575) covalent geometry : bond 0.00320 ( 5927) covalent geometry : angle 0.60837 ( 8283) *********************** 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 : 0.560 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: 0.2824 time to fit residues: 30.6038 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 : 0.531 ------------------------------------------------------------------------------- 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 50 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 0.0980 chunk 24 optimal weight: 0.5980 chunk 47 optimal weight: 7.9990 chunk 18 optimal weight: 0.0870 chunk 28 optimal weight: 0.0970 chunk 35 optimal weight: 0.0270 chunk 54 optimal weight: 0.9990 overall best weight: 0.1814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 127 GLN A 203 GLN A 269 ASN A 383 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.161733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.126648 restraints weight = 8134.362| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.69 r_work: 0.3421 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5927 Z= 0.133 Angle : 0.612 11.183 8283 Z= 0.315 Chirality : 0.041 0.132 940 Planarity : 0.006 0.049 852 Dihedral : 23.056 177.355 1420 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.10 % Allowed : 8.82 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.36), residues: 553 helix: 0.44 (0.35), residues: 225 sheet: -0.26 (0.70), residues: 55 loop : -0.54 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 318 HIS 0.003 0.001 HIS A 498 PHE 0.011 0.001 PHE A 635 TYR 0.010 0.001 TYR A 432 ARG 0.006 0.000 ARG A 585 Details of bonding type rmsd hydrogen bonds : bond 0.05133 ( 211) hydrogen bonds : angle 4.97545 ( 575) covalent geometry : bond 0.00292 ( 5927) covalent geometry : angle 0.61167 ( 8283) *********************** 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 93 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 ASN cc_start: 0.6698 (OUTLIER) cc_final: 0.6470 (p0) REVERT: A 185 ASP cc_start: 0.7271 (t0) cc_final: 0.6927 (t0) REVERT: A 403 ARG cc_start: 0.8059 (mtm180) cc_final: 0.7792 (mtm180) REVERT: A 431 ARG cc_start: 0.7546 (mtm110) cc_final: 0.7148 (mtm180) REVERT: A 514 SER cc_start: 0.6331 (OUTLIER) cc_final: 0.5918 (t) REVERT: A 582 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7142 (mm-30) outliers start: 10 outliers final: 7 residues processed: 89 average time/residue: 0.3084 time to fit residues: 33.0652 Evaluate side-chains 86 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN 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 203 GLN Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 416 LEU 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 14 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 2 optimal weight: 0.3980 chunk 53 optimal weight: 0.7980 chunk 16 optimal weight: 0.0770 chunk 24 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 127 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.158622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.123480 restraints weight = 8195.684| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.71 r_work: 0.3358 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1481 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= 0.174 Angle : 0.587 10.017 8283 Z= 0.306 Chirality : 0.041 0.136 940 Planarity : 0.005 0.051 852 Dihedral : 22.962 179.186 1420 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.94 % Allowed : 10.71 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.36), residues: 553 helix: 0.26 (0.34), residues: 231 sheet: -0.37 (0.66), residues: 55 loop : -0.51 (0.40), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 318 HIS 0.003 0.001 HIS A 498 PHE 0.007 0.001 PHE A 102 TYR 0.012 0.002 TYR A 432 ARG 0.005 0.000 ARG A 585 Details of bonding type rmsd hydrogen bonds : bond 0.05049 ( 211) hydrogen bonds : angle 4.74956 ( 575) covalent geometry : bond 0.00390 ( 5927) covalent geometry : angle 0.58698 ( 8283) *********************** 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 95 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: A 431 ARG cc_start: 0.7571 (mtm110) cc_final: 0.7109 (mtm180) REVERT: A 514 SER cc_start: 0.6417 (OUTLIER) cc_final: 0.5971 (t) REVERT: A 560 GLU cc_start: 0.6491 (mp0) cc_final: 0.6258 (mp0) REVERT: A 582 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7496 (mm-30) outliers start: 14 outliers final: 6 residues processed: 90 average time/residue: 0.2718 time to fit residues: 29.7541 Evaluate side-chains 87 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 372 GLU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 34 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 42 optimal weight: 0.0770 chunk 35 optimal weight: 0.2980 chunk 37 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 16 optimal weight: 0.0270 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.160001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.124782 restraints weight = 8258.955| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.77 r_work: 0.3362 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.1714 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= 0.136 Angle : 0.557 9.412 8283 Z= 0.291 Chirality : 0.040 0.130 940 Planarity : 0.005 0.050 852 Dihedral : 22.961 178.579 1414 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.15 % Allowed : 11.13 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.36), residues: 553 helix: 0.50 (0.34), residues: 230 sheet: -0.18 (0.67), residues: 55 loop : -0.47 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 318 HIS 0.003 0.001 HIS A 498 PHE 0.006 0.001 PHE A 102 TYR 0.012 0.001 TYR A 432 ARG 0.009 0.000 ARG A 585 Details of bonding type rmsd hydrogen bonds : bond 0.04370 ( 211) hydrogen bonds : angle 4.49165 ( 575) covalent geometry : bond 0.00299 ( 5927) covalent geometry : angle 0.55687 ( 8283) *********************** 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 98 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 185 ASP cc_start: 0.7323 (t0) cc_final: 0.6981 (t0) REVERT: A 431 ARG cc_start: 0.7553 (mtm110) cc_final: 0.7053 (mtm180) REVERT: A 514 SER cc_start: 0.6681 (OUTLIER) cc_final: 0.6308 (t) REVERT: A 560 GLU cc_start: 0.6511 (mp0) cc_final: 0.6226 (mp0) REVERT: A 582 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7416 (mm-30) outliers start: 15 outliers final: 10 residues processed: 91 average time/residue: 0.2774 time to fit residues: 30.4338 Evaluate side-chains 92 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 148 GLU 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 465 MET 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 23 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 16 optimal weight: 0.0020 chunk 13 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 chunk 18 optimal weight: 0.2980 chunk 31 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- 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 = 0.3961 r_free = 0.3961 target = 0.159151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.123833 restraints weight = 8158.668| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.69 r_work: 0.3376 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5927 Z= 0.163 Angle : 0.567 9.072 8283 Z= 0.297 Chirality : 0.041 0.131 940 Planarity : 0.005 0.051 852 Dihedral : 22.879 178.844 1410 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.36 % Allowed : 11.97 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.36), residues: 553 helix: 0.59 (0.34), residues: 230 sheet: -0.07 (0.63), residues: 65 loop : -0.50 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 318 HIS 0.003 0.001 HIS A 498 PHE 0.007 0.001 PHE A 102 TYR 0.012 0.002 TYR A 432 ARG 0.008 0.000 ARG A 585 Details of bonding type rmsd hydrogen bonds : bond 0.04461 ( 211) hydrogen bonds : angle 4.42565 ( 575) covalent geometry : bond 0.00368 ( 5927) covalent geometry : angle 0.56701 ( 8283) *********************** 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 94 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: A 157 LYS cc_start: 0.6695 (OUTLIER) cc_final: 0.6317 (mttp) REVERT: A 431 ARG cc_start: 0.7612 (mtm110) cc_final: 0.7095 (mtm180) REVERT: A 446 GLU cc_start: 0.5707 (OUTLIER) cc_final: 0.5426 (pm20) REVERT: A 560 GLU cc_start: 0.6517 (mp0) cc_final: 0.6283 (mp0) REVERT: A 582 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7484 (mm-30) outliers start: 16 outliers final: 10 residues processed: 87 average time/residue: 0.2697 time to fit residues: 28.7485 Evaluate side-chains 88 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 344 LYS 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 446 GLU 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 30 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 0.4980 chunk 42 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 54 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.159075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.123763 restraints weight = 8095.971| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.67 r_work: 0.3379 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1934 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= 0.174 Angle : 0.604 19.118 8283 Z= 0.302 Chirality : 0.041 0.132 940 Planarity : 0.006 0.051 852 Dihedral : 22.915 178.933 1409 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.36 % Allowed : 12.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.36), residues: 553 helix: 0.60 (0.34), residues: 230 sheet: -0.11 (0.63), residues: 65 loop : -0.54 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 318 HIS 0.003 0.001 HIS A 498 PHE 0.007 0.001 PHE A 102 TYR 0.012 0.002 TYR A 432 ARG 0.009 0.000 ARG A 585 Details of bonding type rmsd hydrogen bonds : bond 0.04501 ( 211) hydrogen bonds : angle 4.38311 ( 575) covalent geometry : bond 0.00392 ( 5927) covalent geometry : angle 0.60394 ( 8283) *********************** 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 100 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: A 72 LEU cc_start: 0.8861 (mt) cc_final: 0.8547 (mp) REVERT: A 123 TYR cc_start: 0.8618 (t80) cc_final: 0.8383 (t80) REVERT: A 157 LYS cc_start: 0.6722 (OUTLIER) cc_final: 0.6359 (mttp) REVERT: A 431 ARG cc_start: 0.7633 (mtm110) cc_final: 0.7131 (mtm180) REVERT: A 560 GLU cc_start: 0.6523 (mp0) cc_final: 0.6284 (mp0) REVERT: A 582 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7516 (mm-30) outliers start: 16 outliers final: 10 residues processed: 91 average time/residue: 0.2545 time to fit residues: 28.1031 Evaluate side-chains 92 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 440 GLU Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 595 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 39 optimal weight: 0.0670 chunk 44 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 13 optimal weight: 0.0870 chunk 34 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 16 optimal weight: 0.0070 chunk 20 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.2914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.160967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.125746 restraints weight = 8188.808| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.73 r_work: 0.3404 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2077 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= 0.129 Angle : 0.575 16.629 8283 Z= 0.288 Chirality : 0.040 0.131 940 Planarity : 0.005 0.051 852 Dihedral : 22.902 178.457 1409 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.94 % Allowed : 13.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.36), residues: 553 helix: 0.78 (0.35), residues: 230 sheet: 0.15 (0.64), residues: 65 loop : -0.49 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 318 HIS 0.003 0.001 HIS A 498 PHE 0.007 0.001 PHE A 102 TYR 0.012 0.001 TYR A 432 ARG 0.009 0.000 ARG A 585 Details of bonding type rmsd hydrogen bonds : bond 0.03975 ( 211) hydrogen bonds : angle 4.21552 ( 575) covalent geometry : bond 0.00286 ( 5927) covalent geometry : angle 0.57494 ( 8283) *********************** 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 97 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 TYR cc_start: 0.8605 (t80) cc_final: 0.8304 (t80) REVERT: A 157 LYS cc_start: 0.6716 (OUTLIER) cc_final: 0.6377 (mttp) REVERT: A 185 ASP cc_start: 0.7281 (t0) cc_final: 0.6955 (t0) REVERT: A 431 ARG cc_start: 0.7582 (mtm110) cc_final: 0.7096 (mtm180) REVERT: A 446 GLU cc_start: 0.5764 (OUTLIER) cc_final: 0.5465 (pm20) REVERT: A 560 GLU cc_start: 0.6538 (mp0) cc_final: 0.6247 (mp0) REVERT: A 582 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7459 (mm-30) outliers start: 14 outliers final: 10 residues processed: 90 average time/residue: 0.2582 time to fit residues: 28.3617 Evaluate side-chains 92 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 374 LEU Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 488 MET 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 35 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 6 optimal weight: 0.0670 chunk 33 optimal weight: 0.9980 chunk 11 optimal weight: 0.2980 chunk 19 optimal weight: 0.0040 chunk 58 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.3730 ------------------------------------------------------------------------------- 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 = 0.3977 r_free = 0.3977 target = 0.160582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.125326 restraints weight = 8077.003| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.68 r_work: 0.3400 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5927 Z= 0.142 Angle : 0.576 16.176 8283 Z= 0.290 Chirality : 0.040 0.131 940 Planarity : 0.005 0.050 852 Dihedral : 22.867 178.839 1409 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.57 % Allowed : 14.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.36), residues: 553 helix: 0.84 (0.35), residues: 230 sheet: 0.15 (0.65), residues: 65 loop : -0.51 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 318 HIS 0.003 0.001 HIS A 498 PHE 0.007 0.001 PHE A 509 TYR 0.013 0.001 TYR A 432 ARG 0.007 0.000 ARG A 585 Details of bonding type rmsd hydrogen bonds : bond 0.04083 ( 211) hydrogen bonds : angle 4.20160 ( 575) covalent geometry : bond 0.00318 ( 5927) covalent geometry : angle 0.57550 ( 8283) *********************** 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 99 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 72 LEU cc_start: 0.8861 (mt) cc_final: 0.8563 (mp) REVERT: A 123 TYR cc_start: 0.8556 (t80) cc_final: 0.8262 (t80) REVERT: A 157 LYS cc_start: 0.6495 (OUTLIER) cc_final: 0.6168 (mttp) REVERT: A 431 ARG cc_start: 0.7594 (mtm110) cc_final: 0.7103 (mtm180) REVERT: A 446 GLU cc_start: 0.5769 (OUTLIER) cc_final: 0.5459 (pm20) REVERT: A 560 GLU cc_start: 0.6544 (mp0) cc_final: 0.6262 (mp0) REVERT: A 582 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7506 (mm-30) outliers start: 17 outliers final: 11 residues processed: 91 average time/residue: 0.2524 time to fit residues: 28.1300 Evaluate side-chains 95 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 374 LEU Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 595 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 44 optimal weight: 7.9990 chunk 7 optimal weight: 0.0770 chunk 36 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 0.3980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.158995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.123681 restraints weight = 8134.011| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.67 r_work: 0.3364 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2187 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= 0.179 Angle : 0.599 15.437 8283 Z= 0.303 Chirality : 0.042 0.134 940 Planarity : 0.005 0.051 852 Dihedral : 22.894 179.164 1409 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.36), residues: 553 helix: 0.77 (0.35), residues: 230 sheet: 0.00 (0.64), residues: 65 loop : -0.53 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 318 HIS 0.003 0.001 HIS A 498 PHE 0.007 0.001 PHE A 102 TYR 0.013 0.002 TYR A 432 ARG 0.010 0.000 ARG A 585 Details of bonding type rmsd hydrogen bonds : bond 0.04444 ( 211) hydrogen bonds : angle 4.27179 ( 575) covalent geometry : bond 0.00406 ( 5927) covalent geometry : angle 0.59906 ( 8283) *********************** 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 : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 LEU cc_start: 0.8865 (mt) cc_final: 0.8547 (mp) REVERT: A 157 LYS cc_start: 0.6502 (OUTLIER) cc_final: 0.6191 (mttp) REVERT: A 203 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7674 (mt0) REVERT: A 431 ARG cc_start: 0.7629 (mtm110) cc_final: 0.7125 (mtm180) REVERT: A 446 GLU cc_start: 0.5743 (OUTLIER) cc_final: 0.5425 (pm20) REVERT: A 560 GLU cc_start: 0.6541 (mp0) cc_final: 0.6283 (mp0) REVERT: A 582 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7539 (mm-30) outliers start: 17 outliers final: 12 residues processed: 88 average time/residue: 0.2516 time to fit residues: 27.1776 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 : 0.502 ------------------------------------------------------------------------------- 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 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 440 GLU Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 488 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 24 optimal weight: 0.4980 chunk 7 optimal weight: 0.0970 chunk 50 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 51 optimal weight: 0.2980 chunk 54 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 19 optimal weight: 0.0970 chunk 57 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 12 optimal weight: 0.3980 overall best weight: 0.2776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.161408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.126471 restraints weight = 8199.432| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.69 r_work: 0.3416 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5927 Z= 0.126 Angle : 0.566 14.935 8283 Z= 0.286 Chirality : 0.040 0.133 940 Planarity : 0.005 0.051 852 Dihedral : 22.881 178.510 1409 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.94 % Allowed : 14.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.37), residues: 553 helix: 0.90 (0.35), residues: 232 sheet: 0.30 (0.66), residues: 65 loop : -0.48 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 318 HIS 0.003 0.001 HIS A 498 PHE 0.007 0.001 PHE A 102 TYR 0.013 0.001 TYR A 432 ARG 0.008 0.000 ARG A 585 Details of bonding type rmsd hydrogen bonds : bond 0.03845 ( 211) hydrogen bonds : angle 4.13244 ( 575) covalent geometry : bond 0.00281 ( 5927) covalent geometry : angle 0.56609 ( 8283) ********************** 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 99 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 72 LEU cc_start: 0.8853 (mt) cc_final: 0.8563 (mp) REVERT: A 139 ARG cc_start: 0.7681 (mtm-85) cc_final: 0.7404 (mtm-85) REVERT: A 157 LYS cc_start: 0.6533 (OUTLIER) cc_final: 0.6238 (mttp) REVERT: A 185 ASP cc_start: 0.7267 (t0) cc_final: 0.6954 (t0) REVERT: A 203 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7628 (mt0) REVERT: A 431 ARG cc_start: 0.7574 (mtm110) cc_final: 0.7104 (mtm180) REVERT: A 446 GLU cc_start: 0.5762 (OUTLIER) cc_final: 0.5444 (pm20) REVERT: A 582 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7457 (mm-30) outliers start: 14 outliers final: 9 residues processed: 90 average time/residue: 0.2578 time to fit residues: 28.2584 Evaluate side-chains 95 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 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 440 GLU Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 554 LEU 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 53 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 36 optimal weight: 0.0870 chunk 52 optimal weight: 0.9990 chunk 14 optimal weight: 0.2980 chunk 57 optimal weight: 0.9990 chunk 17 optimal weight: 0.0010 chunk 33 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 overall best weight: 0.4164 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.160401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.125064 restraints weight = 8177.517| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.73 r_work: 0.3391 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5927 Z= 0.152 Angle : 0.578 14.698 8283 Z= 0.293 Chirality : 0.040 0.131 940 Planarity : 0.005 0.051 852 Dihedral : 22.858 179.055 1409 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.94 % Allowed : 15.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.37), residues: 553 helix: 0.89 (0.35), residues: 232 sheet: 0.19 (0.66), residues: 65 loop : -0.47 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 318 HIS 0.003 0.001 HIS A 498 PHE 0.007 0.001 PHE A 102 TYR 0.017 0.002 TYR A 578 ARG 0.010 0.000 ARG A 585 Details of bonding type rmsd hydrogen bonds : bond 0.04094 ( 211) hydrogen bonds : angle 4.15959 ( 575) covalent geometry : bond 0.00343 ( 5927) covalent geometry : angle 0.57812 ( 8283) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4157.94 seconds wall clock time: 72 minutes 45.53 seconds (4365.53 seconds total)