Starting phenix.real_space_refine on Wed Sep 17 05:27:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v0q_26948/09_2025/7v0q_26948.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v0q_26948/09_2025/7v0q_26948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v0q_26948/09_2025/7v0q_26948.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v0q_26948/09_2025/7v0q_26948.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v0q_26948/09_2025/7v0q_26948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v0q_26948/09_2025/7v0q_26948.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.249 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: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 3282 2.51 5 N 916 2.21 5 O 1080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5301 Number of models: 1 Model: "" Number of chains: 2 Chain: "X" Number of atoms: 5174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5174 Classifications: {'peptide': 658} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 30, 'TRANS': 627} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "X" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 127 Classifications: {'water': 127} Link IDs: {None: 126} Time building chain proxies: 1.48, per 1000 atoms: 0.28 Number of scatterers: 5301 At special positions: 0 Unit cell: (98.355, 101.675, 73.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 23 16.00 O 1080 8.00 N 916 7.00 C 3282 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: 0.45 Conformation dependent library (CDL) restraints added in 214.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1234 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 10 sheets defined 21.3% alpha, 36.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'X' and resid 13 through 21 Processing helix chain 'X' and resid 51 through 58 removed outlier: 3.570A pdb=" N ALA X 55 " --> pdb=" O ALA X 51 " (cutoff:3.500A) Processing helix chain 'X' and resid 151 through 159 Processing helix chain 'X' and resid 187 through 197 Processing helix chain 'X' and resid 201 through 206 removed outlier: 4.047A pdb=" N SER X 206 " --> pdb=" O GLU X 203 " (cutoff:3.500A) Processing helix chain 'X' and resid 207 through 227 Processing helix chain 'X' and resid 247 through 258 removed outlier: 4.141A pdb=" N ILE X 251 " --> pdb=" O GLY X 247 " (cutoff:3.500A) Processing helix chain 'X' and resid 264 through 268 Processing helix chain 'X' and resid 269 through 283 removed outlier: 4.344A pdb=" N ALA X 273 " --> pdb=" O TRP X 269 " (cutoff:3.500A) Processing helix chain 'X' and resid 368 through 374 Processing helix chain 'X' and resid 381 through 389 removed outlier: 3.661A pdb=" N ILE X 389 " --> pdb=" O LEU X 385 " (cutoff:3.500A) Processing helix chain 'X' and resid 431 through 436 removed outlier: 3.914A pdb=" N TYR X 435 " --> pdb=" O ILE X 431 " (cutoff:3.500A) Processing helix chain 'X' and resid 441 through 459 Processing helix chain 'X' and resid 550 through 552 No H-bonds generated for 'chain 'X' and resid 550 through 552' Processing sheet with id=AA1, first strand: chain 'X' and resid 7 through 11 removed outlier: 6.826A pdb=" N TYR X 44 " --> pdb=" O LYS X 8 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N CYS X 10 " --> pdb=" O ILE X 42 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE X 42 " --> pdb=" O CYS X 10 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N SER X 105 " --> pdb=" O VAL X 94 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N VAL X 94 " --> pdb=" O SER X 105 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N THR X 107 " --> pdb=" O ALA X 92 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ALA X 92 " --> pdb=" O THR X 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'X' and resid 31 through 34 removed outlier: 4.709A pdb=" N LEU X 31 " --> pdb=" O GLN X 133 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LEU X 130 " --> pdb=" O LEU X 121 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU X 121 " --> pdb=" O LEU X 130 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY X 132 " --> pdb=" O LEU X 119 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'X' and resid 163 through 169 Processing sheet with id=AA4, first strand: chain 'X' and resid 362 through 367 removed outlier: 3.804A pdb=" N SER X 362 " --> pdb=" O SER X 352 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N THR X 330 " --> pdb=" O LEU X 349 " (cutoff:3.500A) removed outlier: 11.935A pdb=" N THR X 328 " --> pdb=" O PRO X 351 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE X 326 " --> pdb=" O PHE X 292 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N PHE X 292 " --> pdb=" O PHE X 326 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N THR X 328 " --> pdb=" O THR X 290 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR X 290 " --> pdb=" O THR X 328 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR X 330 " --> pdb=" O VAL X 288 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL X 288 " --> pdb=" O THR X 330 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N CYS X 332 " --> pdb=" O ALA X 286 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA X 286 " --> pdb=" O CYS X 332 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N VAL X 288 " --> pdb=" O THR X 420 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N THR X 420 " --> pdb=" O VAL X 288 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR X 290 " --> pdb=" O ILE X 418 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE X 418 " --> pdb=" O THR X 290 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'X' and resid 303 through 309 removed outlier: 5.992A pdb=" N ILE X 304 " --> pdb=" O VAL X 394 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N TRP X 396 " --> pdb=" O ILE X 304 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLU X 306 " --> pdb=" O TRP X 396 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N CYS X 398 " --> pdb=" O GLU X 306 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TYR X 308 " --> pdb=" O CYS X 398 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'X' and resid 408 through 409 removed outlier: 6.337A pdb=" N ASP X 408 " --> pdb=" O PHE X 578 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N GLN X 580 " --> pdb=" O ASP X 408 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU X 485 " --> pdb=" O CYS X 586 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'X' and resid 408 through 409 removed outlier: 6.337A pdb=" N ASP X 408 " --> pdb=" O PHE X 578 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N GLN X 580 " --> pdb=" O ASP X 408 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LYS X 505 " --> pdb=" O THR X 534 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N THR X 534 " --> pdb=" O LYS X 505 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL X 507 " --> pdb=" O HIS X 532 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N HIS X 532 " --> pdb=" O VAL X 507 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU X 509 " --> pdb=" O LYS X 530 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LYS X 530 " --> pdb=" O LEU X 509 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE X 511 " --> pdb=" O ARG X 528 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG X 528 " --> pdb=" O ILE X 511 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL X 513 " --> pdb=" O LEU X 526 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'X' and resid 475 through 480 Processing sheet with id=AA9, first strand: chain 'X' and resid 590 through 593 Processing sheet with id=AB1, first strand: chain 'X' and resid 597 through 599 removed outlier: 6.518A pdb=" N ALA X 598 " --> pdb=" O VAL X 685 " (cutoff:3.500A) 201 hydrogen bonds defined for protein. 558 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.83 Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1719 1.34 - 1.46: 1130 1.46 - 1.58: 2401 1.58 - 1.70: 0 1.70 - 1.82: 31 Bond restraints: 5281 Sorted by residual: bond pdb=" N GLY X 489 " pdb=" CA GLY X 489 " ideal model delta sigma weight residual 1.449 1.436 0.013 1.45e-02 4.76e+03 8.03e-01 bond pdb=" CA ILE X 81 " pdb=" CB ILE X 81 " ideal model delta sigma weight residual 1.531 1.541 -0.009 1.16e-02 7.43e+03 6.56e-01 bond pdb=" CA SER X 473 " pdb=" C SER X 473 " ideal model delta sigma weight residual 1.525 1.542 -0.017 2.10e-02 2.27e+03 6.46e-01 bond pdb=" C ASP X 344 " pdb=" N GLY X 345 " ideal model delta sigma weight residual 1.335 1.329 0.006 7.50e-03 1.78e+04 6.43e-01 bond pdb=" CB GLU X 144 " pdb=" CG GLU X 144 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.31e-01 ... (remaining 5276 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 7041 1.83 - 3.65: 107 3.65 - 5.48: 14 5.48 - 7.31: 3 7.31 - 9.13: 1 Bond angle restraints: 7166 Sorted by residual: angle pdb=" N GLY X 345 " pdb=" CA GLY X 345 " pdb=" C GLY X 345 " ideal model delta sigma weight residual 111.21 114.15 -2.94 1.04e+00 9.25e-01 8.01e+00 angle pdb=" CA LEU X 475 " pdb=" CB LEU X 475 " pdb=" CG LEU X 475 " ideal model delta sigma weight residual 116.30 125.43 -9.13 3.50e+00 8.16e-02 6.81e+00 angle pdb=" CB MET X 672 " pdb=" CG MET X 672 " pdb=" SD MET X 672 " ideal model delta sigma weight residual 112.70 119.53 -6.83 3.00e+00 1.11e-01 5.19e+00 angle pdb=" CD ARG X 16 " pdb=" NE ARG X 16 " pdb=" CZ ARG X 16 " ideal model delta sigma weight residual 124.40 127.52 -3.12 1.40e+00 5.10e-01 4.97e+00 angle pdb=" N PRO X 556 " pdb=" CD PRO X 556 " pdb=" CG PRO X 556 " ideal model delta sigma weight residual 103.20 100.01 3.19 1.50e+00 4.44e-01 4.51e+00 ... (remaining 7161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 2786 17.85 - 35.69: 252 35.69 - 53.53: 95 53.53 - 71.38: 31 71.38 - 89.22: 17 Dihedral angle restraints: 3181 sinusoidal: 1277 harmonic: 1904 Sorted by residual: dihedral pdb=" CA ILE X 418 " pdb=" C ILE X 418 " pdb=" N SER X 419 " pdb=" CA SER X 419 " ideal model delta harmonic sigma weight residual -180.00 -162.43 -17.57 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CG ARG X 16 " pdb=" CD ARG X 16 " pdb=" NE ARG X 16 " pdb=" CZ ARG X 16 " ideal model delta sinusoidal sigma weight residual 90.00 41.19 48.81 2 1.50e+01 4.44e-03 1.21e+01 dihedral pdb=" CA LYS X 436 " pdb=" C LYS X 436 " pdb=" N TYR X 437 " pdb=" CA TYR X 437 " ideal model delta harmonic sigma weight residual 180.00 163.48 16.52 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 3178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 453 0.029 - 0.057: 225 0.057 - 0.086: 78 0.086 - 0.114: 42 0.114 - 0.143: 13 Chirality restraints: 811 Sorted by residual: chirality pdb=" CB THR X 407 " pdb=" CA THR X 407 " pdb=" OG1 THR X 407 " pdb=" CG2 THR X 407 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CA ILE X 631 " pdb=" N ILE X 631 " pdb=" C ILE X 631 " pdb=" CB ILE X 631 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CG LEU X 531 " pdb=" CB LEU X 531 " pdb=" CD1 LEU X 531 " pdb=" CD2 LEU X 531 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 808 not shown) Planarity restraints: 923 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN X 555 " -0.027 5.00e-02 4.00e+02 3.99e-02 2.54e+00 pdb=" N PRO X 556 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO X 556 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO X 556 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU X 339 " -0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO X 340 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO X 340 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO X 340 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG X 16 " 0.108 9.50e-02 1.11e+02 4.89e-02 1.87e+00 pdb=" NE ARG X 16 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG X 16 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG X 16 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG X 16 " 0.000 2.00e-02 2.50e+03 ... (remaining 920 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 722 2.76 - 3.30: 4743 3.30 - 3.83: 9669 3.83 - 4.37: 11275 4.37 - 4.90: 19023 Nonbonded interactions: 45432 Sorted by model distance: nonbonded pdb=" OE2 GLU X 331 " pdb=" OH TYR X 435 " model vdw 2.227 3.040 nonbonded pdb=" O PRO X 557 " pdb=" OG1 THR X 560 " model vdw 2.281 3.040 nonbonded pdb=" O LEU X 349 " pdb=" O HOH X 701 " model vdw 2.291 3.040 nonbonded pdb=" O LEU X 160 " pdb=" O HOH X 702 " model vdw 2.292 3.040 nonbonded pdb=" O ARG X 628 " pdb=" O HOH X 703 " model vdw 2.293 3.040 ... (remaining 45427 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.000 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 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 0.039 5281 Z= 0.160 Angle : 0.606 9.133 7166 Z= 0.320 Chirality : 0.043 0.143 811 Planarity : 0.005 0.049 923 Dihedral : 18.362 89.222 1947 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.15 % Allowed : 19.32 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.32), residues: 650 helix: 1.96 (0.47), residues: 114 sheet: 1.16 (0.32), residues: 255 loop : 0.80 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG X 16 TYR 0.021 0.002 TYR X 167 PHE 0.019 0.002 PHE X 639 TRP 0.005 0.001 TRP X 205 HIS 0.005 0.001 HIS X 500 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 5281) covalent geometry : angle 0.60567 ( 7166) hydrogen bonds : bond 0.14348 ( 201) hydrogen bonds : angle 7.53892 ( 558) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.239 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 103 average time/residue: 0.7640 time to fit residues: 81.2625 Evaluate side-chains 100 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 88 LYS Chi-restraints excluded: chain X residue 120 LEU Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 407 THR Chi-restraints excluded: chain X residue 522 LEU Chi-restraints excluded: chain X residue 533 LEU Chi-restraints excluded: chain X residue 641 SER Chi-restraints excluded: chain X residue 659 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 62 optimal weight: 0.0870 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 13 GLN X 128 GLN X 175 GLN X 492 GLN X 600 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.125151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.103106 restraints weight = 5125.074| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.23 r_work: 0.2891 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.0713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5281 Z= 0.097 Angle : 0.481 5.704 7166 Z= 0.252 Chirality : 0.041 0.139 811 Planarity : 0.004 0.034 923 Dihedral : 5.791 58.124 726 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 3.94 % Allowed : 18.25 % Favored : 77.82 % 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 aren not related in a simple way. whole: 1.95 (0.33), residues: 650 helix: 2.35 (0.48), residues: 115 sheet: 1.34 (0.32), residues: 253 loop : 0.96 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 16 TYR 0.012 0.001 TYR X 167 PHE 0.015 0.001 PHE X 639 TRP 0.007 0.001 TRP X 324 HIS 0.002 0.001 HIS X 210 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 5281) covalent geometry : angle 0.48142 ( 7166) hydrogen bonds : bond 0.03764 ( 201) hydrogen bonds : angle 5.64241 ( 558) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.233 Fit side-chains REVERT: X 128 GLN cc_start: 0.7417 (mt0) cc_final: 0.7111 (tt0) REVERT: X 341 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7723 (tp40) REVERT: X 503 GLN cc_start: 0.5393 (OUTLIER) cc_final: 0.5116 (pm20) REVERT: X 505 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7981 (ttmt) outliers start: 22 outliers final: 9 residues processed: 102 average time/residue: 0.7523 time to fit residues: 79.2320 Evaluate side-chains 105 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 159 LEU Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 298 THR Chi-restraints excluded: chain X residue 341 GLN Chi-restraints excluded: chain X residue 384 ASP Chi-restraints excluded: chain X residue 407 THR Chi-restraints excluded: chain X residue 456 MET Chi-restraints excluded: chain X residue 503 GLN Chi-restraints excluded: chain X residue 505 LYS Chi-restraints excluded: chain X residue 533 LEU Chi-restraints excluded: chain X residue 611 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 55 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 13 GLN X 142 ASN X 175 GLN X 416 ASN X 492 GLN X 508 GLN X 600 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.125052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.102848 restraints weight = 5009.508| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.22 r_work: 0.2898 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5281 Z= 0.095 Angle : 0.465 5.248 7166 Z= 0.241 Chirality : 0.041 0.136 811 Planarity : 0.003 0.033 923 Dihedral : 5.176 56.177 716 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.40 % Allowed : 19.14 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.33), residues: 650 helix: 2.44 (0.48), residues: 115 sheet: 1.37 (0.32), residues: 248 loop : 0.92 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG X 16 TYR 0.013 0.001 TYR X 167 PHE 0.015 0.001 PHE X 639 TRP 0.005 0.001 TRP X 527 HIS 0.002 0.001 HIS X 517 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 5281) covalent geometry : angle 0.46492 ( 7166) hydrogen bonds : bond 0.03401 ( 201) hydrogen bonds : angle 5.36686 ( 558) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.163 Fit side-chains REVERT: X 127 LYS cc_start: 0.7262 (pptt) cc_final: 0.7044 (pptt) REVERT: X 128 GLN cc_start: 0.7394 (mt0) cc_final: 0.7164 (tt0) REVERT: X 341 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.7691 (tp40) REVERT: X 508 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7517 (tm130) outliers start: 19 outliers final: 8 residues processed: 100 average time/residue: 0.7357 time to fit residues: 75.9717 Evaluate side-chains 99 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 159 LEU Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 298 THR Chi-restraints excluded: chain X residue 341 GLN Chi-restraints excluded: chain X residue 384 ASP Chi-restraints excluded: chain X residue 407 THR Chi-restraints excluded: chain X residue 456 MET Chi-restraints excluded: chain X residue 508 GLN Chi-restraints excluded: chain X residue 659 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 27 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 45 optimal weight: 0.0050 chunk 48 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 35 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 overall best weight: 1.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 13 GLN X 175 GLN X 492 GLN X 600 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.124345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.101959 restraints weight = 4989.038| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.23 r_work: 0.2884 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5281 Z= 0.111 Angle : 0.479 5.314 7166 Z= 0.248 Chirality : 0.042 0.136 811 Planarity : 0.004 0.035 923 Dihedral : 4.875 54.549 714 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.76 % Allowed : 19.14 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.33), residues: 650 helix: 2.44 (0.48), residues: 115 sheet: 1.32 (0.32), residues: 248 loop : 0.93 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 16 TYR 0.014 0.001 TYR X 167 PHE 0.016 0.001 PHE X 639 TRP 0.003 0.001 TRP X 527 HIS 0.003 0.001 HIS X 517 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 5281) covalent geometry : angle 0.47894 ( 7166) hydrogen bonds : bond 0.03433 ( 201) hydrogen bonds : angle 5.35939 ( 558) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.233 Fit side-chains REVERT: X 341 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7695 (tp40) outliers start: 21 outliers final: 11 residues processed: 99 average time/residue: 0.7189 time to fit residues: 73.5908 Evaluate side-chains 102 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 159 LEU Chi-restraints excluded: chain X residue 175 GLN Chi-restraints excluded: chain X residue 177 GLU Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 298 THR Chi-restraints excluded: chain X residue 341 GLN Chi-restraints excluded: chain X residue 384 ASP Chi-restraints excluded: chain X residue 407 THR Chi-restraints excluded: chain X residue 456 MET Chi-restraints excluded: chain X residue 533 LEU Chi-restraints excluded: chain X residue 659 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 23 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 61 optimal weight: 0.1980 chunk 5 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 13 GLN X 128 GLN X 142 ASN X 175 GLN X 492 GLN X 508 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.121911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.099490 restraints weight = 5103.034| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.23 r_work: 0.2845 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.0819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5281 Z= 0.159 Angle : 0.527 5.491 7166 Z= 0.275 Chirality : 0.043 0.142 811 Planarity : 0.004 0.037 923 Dihedral : 5.124 54.615 714 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 4.65 % Allowed : 18.60 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.33), residues: 650 helix: 2.34 (0.48), residues: 115 sheet: 1.25 (0.32), residues: 248 loop : 0.87 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 16 TYR 0.018 0.002 TYR X 167 PHE 0.021 0.002 PHE X 639 TRP 0.005 0.001 TRP X 205 HIS 0.004 0.001 HIS X 500 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 5281) covalent geometry : angle 0.52667 ( 7166) hydrogen bonds : bond 0.03914 ( 201) hydrogen bonds : angle 5.53093 ( 558) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.197 Fit side-chains REVERT: X 341 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7755 (tp40) outliers start: 26 outliers final: 13 residues processed: 108 average time/residue: 0.7396 time to fit residues: 82.3841 Evaluate side-chains 112 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 83 SER Chi-restraints excluded: chain X residue 96 GLU Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 159 LEU Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 298 THR Chi-restraints excluded: chain X residue 341 GLN Chi-restraints excluded: chain X residue 384 ASP Chi-restraints excluded: chain X residue 407 THR Chi-restraints excluded: chain X residue 522 LEU Chi-restraints excluded: chain X residue 533 LEU Chi-restraints excluded: chain X residue 648 MET Chi-restraints excluded: chain X residue 649 CYS Chi-restraints excluded: chain X residue 659 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 45 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 4 optimal weight: 0.0050 chunk 31 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 overall best weight: 2.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 13 GLN X 128 GLN X 175 GLN X 492 GLN X 538 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.121391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.099139 restraints weight = 5095.323| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.22 r_work: 0.2839 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5281 Z= 0.161 Angle : 0.531 5.586 7166 Z= 0.278 Chirality : 0.043 0.143 811 Planarity : 0.004 0.036 923 Dihedral : 5.191 53.254 714 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 4.29 % Allowed : 18.60 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.33), residues: 650 helix: 2.30 (0.48), residues: 115 sheet: 1.14 (0.32), residues: 251 loop : 0.91 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG X 16 TYR 0.020 0.002 TYR X 167 PHE 0.023 0.002 PHE X 639 TRP 0.005 0.001 TRP X 205 HIS 0.004 0.001 HIS X 22 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 5281) covalent geometry : angle 0.53142 ( 7166) hydrogen bonds : bond 0.03927 ( 201) hydrogen bonds : angle 5.55406 ( 558) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.240 Fit side-chains REVERT: X 341 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7751 (tp40) REVERT: X 529 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8143 (tptp) outliers start: 24 outliers final: 13 residues processed: 111 average time/residue: 0.7573 time to fit residues: 86.7473 Evaluate side-chains 110 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 83 SER Chi-restraints excluded: chain X residue 96 GLU Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 159 LEU Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 298 THR Chi-restraints excluded: chain X residue 341 GLN Chi-restraints excluded: chain X residue 384 ASP Chi-restraints excluded: chain X residue 407 THR Chi-restraints excluded: chain X residue 508 GLN Chi-restraints excluded: chain X residue 522 LEU Chi-restraints excluded: chain X residue 529 LYS Chi-restraints excluded: chain X residue 533 LEU Chi-restraints excluded: chain X residue 649 CYS Chi-restraints excluded: chain X residue 659 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 2 optimal weight: 0.0470 chunk 18 optimal weight: 0.6980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 13 GLN X 142 ASN X 175 GLN X 492 GLN X 602 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.125732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.103470 restraints weight = 5100.585| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.24 r_work: 0.2903 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5281 Z= 0.089 Angle : 0.468 6.371 7166 Z= 0.241 Chirality : 0.041 0.134 811 Planarity : 0.003 0.031 923 Dihedral : 4.731 48.768 714 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.22 % Allowed : 20.21 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.33), residues: 650 helix: 2.50 (0.49), residues: 115 sheet: 1.22 (0.32), residues: 247 loop : 0.99 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG X 16 TYR 0.012 0.001 TYR X 167 PHE 0.014 0.001 PHE X 639 TRP 0.007 0.001 TRP X 527 HIS 0.002 0.001 HIS X 517 Details of bonding type rmsd covalent geometry : bond 0.00194 ( 5281) covalent geometry : angle 0.46805 ( 7166) hydrogen bonds : bond 0.02988 ( 201) hydrogen bonds : angle 5.19297 ( 558) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.249 Fit side-chains REVERT: X 226 ARG cc_start: 0.8611 (mmt90) cc_final: 0.8329 (mtp85) REVERT: X 341 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7681 (tp40) outliers start: 18 outliers final: 10 residues processed: 100 average time/residue: 0.7484 time to fit residues: 77.1867 Evaluate side-chains 101 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 83 SER Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 159 LEU Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 298 THR Chi-restraints excluded: chain X residue 341 GLN Chi-restraints excluded: chain X residue 384 ASP Chi-restraints excluded: chain X residue 407 THR Chi-restraints excluded: chain X residue 456 MET Chi-restraints excluded: chain X residue 522 LEU Chi-restraints excluded: chain X residue 533 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 43 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 13 GLN X 175 GLN X 492 GLN X 508 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.121891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.099596 restraints weight = 5035.621| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.22 r_work: 0.2851 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5281 Z= 0.152 Angle : 0.530 6.421 7166 Z= 0.274 Chirality : 0.043 0.141 811 Planarity : 0.004 0.039 923 Dihedral : 5.057 51.545 714 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.40 % Allowed : 20.57 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.33), residues: 650 helix: 2.34 (0.48), residues: 115 sheet: 1.23 (0.32), residues: 245 loop : 0.93 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 16 TYR 0.019 0.002 TYR X 167 PHE 0.021 0.002 PHE X 639 TRP 0.005 0.001 TRP X 205 HIS 0.004 0.001 HIS X 22 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 5281) covalent geometry : angle 0.53000 ( 7166) hydrogen bonds : bond 0.03751 ( 201) hydrogen bonds : angle 5.45373 ( 558) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.223 Fit side-chains REVERT: X 341 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7739 (tp40) REVERT: X 529 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.7478 (tppp) outliers start: 19 outliers final: 11 residues processed: 106 average time/residue: 0.8005 time to fit residues: 87.4185 Evaluate side-chains 108 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 83 SER Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 159 LEU Chi-restraints excluded: chain X residue 175 GLN Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 298 THR Chi-restraints excluded: chain X residue 341 GLN Chi-restraints excluded: chain X residue 384 ASP Chi-restraints excluded: chain X residue 407 THR Chi-restraints excluded: chain X residue 522 LEU Chi-restraints excluded: chain X residue 529 LYS Chi-restraints excluded: chain X residue 533 LEU Chi-restraints excluded: chain X residue 659 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 2 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 13 GLN X 142 ASN X 175 GLN X 492 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.123563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.101390 restraints weight = 5111.893| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.22 r_work: 0.2880 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5281 Z= 0.107 Angle : 0.508 7.039 7166 Z= 0.261 Chirality : 0.042 0.140 811 Planarity : 0.004 0.038 923 Dihedral : 4.833 48.535 714 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.86 % Allowed : 21.29 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.33), residues: 650 helix: 2.49 (0.49), residues: 114 sheet: 1.23 (0.32), residues: 248 loop : 0.98 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG X 16 TYR 0.015 0.001 TYR X 167 PHE 0.018 0.001 PHE X 639 TRP 0.006 0.001 TRP X 527 HIS 0.002 0.001 HIS X 22 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 5281) covalent geometry : angle 0.50766 ( 7166) hydrogen bonds : bond 0.03248 ( 201) hydrogen bonds : angle 5.28698 ( 558) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.145 Fit side-chains REVERT: X 175 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7882 (mp-120) REVERT: X 341 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7698 (tp40) REVERT: X 529 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8115 (tptp) outliers start: 16 outliers final: 9 residues processed: 103 average time/residue: 0.7719 time to fit residues: 82.0728 Evaluate side-chains 104 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 83 SER Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 159 LEU Chi-restraints excluded: chain X residue 175 GLN Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 298 THR Chi-restraints excluded: chain X residue 341 GLN Chi-restraints excluded: chain X residue 384 ASP Chi-restraints excluded: chain X residue 407 THR Chi-restraints excluded: chain X residue 522 LEU Chi-restraints excluded: chain X residue 529 LYS Chi-restraints excluded: chain X residue 533 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 5 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 9 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 13 GLN X 175 GLN X 492 GLN X 508 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.121882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.099420 restraints weight = 5103.046| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.23 r_work: 0.2848 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5281 Z= 0.159 Angle : 0.546 7.265 7166 Z= 0.282 Chirality : 0.043 0.142 811 Planarity : 0.004 0.041 923 Dihedral : 5.061 50.254 714 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.86 % Allowed : 21.29 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.33), residues: 650 helix: 2.42 (0.48), residues: 114 sheet: 1.22 (0.32), residues: 245 loop : 0.93 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 16 TYR 0.019 0.002 TYR X 167 PHE 0.024 0.002 PHE X 639 TRP 0.006 0.001 TRP X 205 HIS 0.004 0.001 HIS X 22 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 5281) covalent geometry : angle 0.54569 ( 7166) hydrogen bonds : bond 0.03783 ( 201) hydrogen bonds : angle 5.47582 ( 558) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.217 Fit side-chains REVERT: X 341 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7736 (tp40) REVERT: X 529 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8105 (tptp) outliers start: 16 outliers final: 8 residues processed: 105 average time/residue: 0.8098 time to fit residues: 87.6635 Evaluate side-chains 106 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 159 LEU Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 298 THR Chi-restraints excluded: chain X residue 341 GLN Chi-restraints excluded: chain X residue 384 ASP Chi-restraints excluded: chain X residue 407 THR Chi-restraints excluded: chain X residue 522 LEU Chi-restraints excluded: chain X residue 529 LYS Chi-restraints excluded: chain X residue 533 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 27 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 4 optimal weight: 6.9990 chunk 12 optimal weight: 0.3980 chunk 54 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 13 GLN X 142 ASN X 175 GLN X 492 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.124661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.102312 restraints weight = 5068.203| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.23 r_work: 0.2889 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 5281 Z= 0.100 Angle : 0.496 7.395 7166 Z= 0.255 Chirality : 0.041 0.133 811 Planarity : 0.004 0.035 923 Dihedral : 4.746 46.638 714 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.50 % Allowed : 21.82 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.33), residues: 650 helix: 2.55 (0.49), residues: 114 sheet: 1.27 (0.32), residues: 245 loop : 1.01 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG X 16 TYR 0.015 0.001 TYR X 167 PHE 0.019 0.001 PHE X 639 TRP 0.007 0.001 TRP X 527 HIS 0.002 0.001 HIS X 517 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 5281) covalent geometry : angle 0.49613 ( 7166) hydrogen bonds : bond 0.03127 ( 201) hydrogen bonds : angle 5.20362 ( 558) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2848.76 seconds wall clock time: 49 minutes 13.10 seconds (2953.10 seconds total)