Starting phenix.real_space_refine on Mon Jun 9 03:01:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c4o_45192/06_2025/9c4o_45192_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c4o_45192/06_2025/9c4o_45192.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c4o_45192/06_2025/9c4o_45192.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c4o_45192/06_2025/9c4o_45192.map" model { file = "/net/cci-nas-00/data/ceres_data/9c4o_45192/06_2025/9c4o_45192_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c4o_45192/06_2025/9c4o_45192_trim.cif" } resolution = 1.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.064 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 S 19 5.16 5 C 3205 2.51 5 N 915 2.21 5 O 1143 1.98 5 H 4883 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10166 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 10030 Classifications: {'peptide': 661} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 633} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 136 Unusual residues: {' CA': 1, 'PQQ': 1} Classifications: {'undetermined': 2, 'water': 111} Link IDs: {None: 112} Time building chain proxies: 5.64, per 1000 atoms: 0.55 Number of scatterers: 10166 At special positions: 0 Unit cell: (86.92, 62.32, 72.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 19 16.00 O 1143 8.00 N 915 7.00 C 3205 6.00 H 4883 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 585 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 674.3 milliseconds 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1178 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 6 sheets defined 6.5% alpha, 53.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 64 through 69 removed outlier: 3.987A pdb=" N THR A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 253 through 260 Processing helix chain 'A' and resid 264 through 271 Processing helix chain 'A' and resid 313 through 318 removed outlier: 3.861A pdb=" N GLN A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 481 removed outlier: 4.264A pdb=" N TYR A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 51 removed outlier: 4.284A pdb=" N ALA A 46 " --> pdb=" O ARG A 137 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN A 132 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ARG A 105 " --> pdb=" O MET A 152 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N VAL A 154 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TYR A 107 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N THR A 156 " --> pdb=" O TYR A 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 77 Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 172 removed outlier: 4.451A pdb=" N TRP A 405 " --> pdb=" O PRO A 349 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR A 351 " --> pdb=" O THR A 403 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR A 403 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR A 353 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU A 401 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLY A 355 " --> pdb=" O PRO A 399 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ASN A 357 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE A 397 " --> pdb=" O ASN A 357 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU A 359 " --> pdb=" O TRP A 395 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N TRP A 395 " --> pdb=" O GLU A 359 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N MET A 361 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU A 393 " --> pdb=" O MET A 361 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLU A 363 " --> pdb=" O ARG A 391 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ARG A 391 " --> pdb=" O GLU A 363 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ARG A 365 " --> pdb=" O ASP A 389 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP A 389 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N GLY A 367 " --> pdb=" O ARG A 387 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N TRP A 447 " --> pdb=" O PHE A 471 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N PHE A 471 " --> pdb=" O TRP A 447 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU A 513 " --> pdb=" O GLN A 556 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLN A 556 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N SER A 515 " --> pdb=" O TRP A 554 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N TRP A 554 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ALA A 517 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU A 552 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N PHE A 519 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ALA A 550 " --> pdb=" O PHE A 519 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N THR A 521 " --> pdb=" O GLN A 548 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N GLN A 548 " --> pdb=" O THR A 521 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N THR A 523 " --> pdb=" O ARG A 546 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ARG A 546 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASP A 525 " --> pdb=" O LYS A 544 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LYS A 544 " --> pdb=" O ASP A 525 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ILE A 527 " --> pdb=" O ALA A 542 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ALA A 542 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL A 529 " --> pdb=" O LYS A 540 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LYS A 540 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE A 562 " --> pdb=" O PHE A 558 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 371 through 373 Processing sheet with id=AA5, first strand: chain 'A' and resid 622 through 623 Processing sheet with id=AA6, first strand: chain 'A' and resid 668 through 671 removed outlier: 3.561A pdb=" N SER A 670 " --> pdb=" O GLU A 682 " (cutoff:3.500A) 280 hydrogen bonds defined for protein. 795 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: 4.21 Time building geometry restraints manager: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4883 1.03 - 1.23: 15 1.23 - 1.42: 2322 1.42 - 1.62: 2914 1.62 - 1.81: 36 Bond restraints: 10170 Sorted by residual: bond pdb=" C PRO A 683 " pdb=" N SER A 684 " ideal model delta sigma weight residual 1.327 1.308 0.018 1.71e-02 3.42e+03 1.16e+00 bond pdb=" CA LYS A 277 " pdb=" C LYS A 277 " ideal model delta sigma weight residual 1.526 1.515 0.011 1.08e-02 8.57e+03 1.03e+00 bond pdb=" C ALA A 450 " pdb=" N GLY A 451 " ideal model delta sigma weight residual 1.330 1.317 0.013 1.32e-02 5.74e+03 9.14e-01 bond pdb=" C GLU A 363 " pdb=" N ASN A 364 " ideal model delta sigma weight residual 1.331 1.318 0.013 1.40e-02 5.10e+03 8.48e-01 bond pdb=" C ARG A 589 " pdb=" N MET A 590 " ideal model delta sigma weight residual 1.326 1.309 0.017 1.84e-02 2.95e+03 8.42e-01 ... (remaining 10165 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 17527 1.29 - 2.58: 613 2.58 - 3.88: 50 3.88 - 5.17: 12 5.17 - 6.46: 2 Bond angle restraints: 18204 Sorted by residual: angle pdb=" N GLY A 492 " pdb=" CA GLY A 492 " pdb=" C GLY A 492 " ideal model delta sigma weight residual 114.67 111.15 3.52 1.10e+00 8.26e-01 1.02e+01 angle pdb=" N ASP A 530 " pdb=" CA ASP A 530 " pdb=" C ASP A 530 " ideal model delta sigma weight residual 111.24 108.22 3.02 1.29e+00 6.01e-01 5.48e+00 angle pdb=" N SER A 375 " pdb=" CA SER A 375 " pdb=" C SER A 375 " ideal model delta sigma weight residual 112.12 108.99 3.13 1.34e+00 5.57e-01 5.46e+00 angle pdb=" N PRO A 685 " pdb=" CA PRO A 685 " pdb=" C PRO A 685 " ideal model delta sigma weight residual 112.47 116.85 -4.38 2.06e+00 2.36e-01 4.52e+00 angle pdb=" CA VAL A 348 " pdb=" C VAL A 348 " pdb=" N PRO A 349 " ideal model delta sigma weight residual 117.33 119.30 -1.97 1.01e+00 9.80e-01 3.82e+00 ... (remaining 18199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 4301 17.76 - 35.52: 360 35.52 - 53.28: 114 53.28 - 71.04: 37 71.04 - 88.80: 16 Dihedral angle restraints: 4828 sinusoidal: 2618 harmonic: 2210 Sorted by residual: dihedral pdb=" CA TYR A 680 " pdb=" C TYR A 680 " pdb=" N TYR A 681 " pdb=" CA TYR A 681 " ideal model delta harmonic sigma weight residual -180.00 -154.89 -25.11 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA PRO A 685 " pdb=" C PRO A 685 " pdb=" N GLY A 686 " pdb=" CA GLY A 686 " ideal model delta harmonic sigma weight residual -180.00 -155.22 -24.78 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA ASP A 398 " pdb=" C ASP A 398 " pdb=" N PRO A 399 " pdb=" CA PRO A 399 " ideal model delta harmonic sigma weight residual 180.00 155.87 24.13 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 4825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 454 0.034 - 0.068: 216 0.068 - 0.102: 45 0.102 - 0.137: 29 0.137 - 0.171: 1 Chirality restraints: 745 Sorted by residual: chirality pdb=" CA PRO A 685 " pdb=" N PRO A 685 " pdb=" C PRO A 685 " pdb=" CB PRO A 685 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.29e-01 chirality pdb=" CA ILE A 501 " pdb=" N ILE A 501 " pdb=" C ILE A 501 " pdb=" CB ILE A 501 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA ILE A 104 " pdb=" N ILE A 104 " pdb=" C ILE A 104 " pdb=" CB ILE A 104 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 ... (remaining 742 not shown) Planarity restraints: 1591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 684 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO A 685 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 685 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 685 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 91 " 0.114 9.50e-02 1.11e+02 3.82e-02 1.62e+00 pdb=" NE ARG A 91 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG A 91 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 91 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 91 " 0.004 2.00e-02 2.50e+03 pdb="HH11 ARG A 91 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 91 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 91 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 91 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 192 " -0.021 5.00e-02 4.00e+02 3.12e-02 1.56e+00 pdb=" N PRO A 193 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 193 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 193 " -0.017 5.00e-02 4.00e+02 ... (remaining 1588 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 714 2.18 - 2.79: 21047 2.79 - 3.39: 30425 3.39 - 4.00: 43620 4.00 - 4.60: 63096 Nonbonded interactions: 158902 Sorted by model distance: nonbonded pdb=" O LEU A 479 " pdb=" H ASN A 490 " model vdw 1.575 2.450 nonbonded pdb=" HH TYR A 481 " pdb=" O2B PQQ A 802 " model vdw 1.583 2.450 nonbonded pdb=" HH TYR A 464 " pdb=" OE2 GLU A 502 " model vdw 1.607 2.450 nonbonded pdb=" O VAL A 638 " pdb=" H LEU A 662 " model vdw 1.616 2.450 nonbonded pdb="HD21 ASN A 357 " pdb=" OE2 GLU A 359 " model vdw 1.627 2.450 ... (remaining 158897 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: 4.200 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: 0.200 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.160 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:14.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 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 0.037 5288 Z= 0.249 Angle : 0.646 6.461 7179 Z= 0.367 Chirality : 0.044 0.171 745 Planarity : 0.005 0.051 958 Dihedral : 16.532 88.799 1925 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.18 % Allowed : 14.76 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.01 (0.32), residues: 659 helix: -1.84 (0.64), residues: 47 sheet: 0.18 (0.25), residues: 349 loop : 0.34 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 568 HIS 0.002 0.001 HIS A 445 PHE 0.016 0.002 PHE A 352 TYR 0.017 0.002 TYR A 681 ARG 0.004 0.001 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.07766 ( 280) hydrogen bonds : angle 6.35315 ( 795) SS BOND : bond 0.00037 ( 1) SS BOND : angle 0.32478 ( 2) covalent geometry : bond 0.00424 ( 5287) covalent geometry : angle 0.64652 ( 7177) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 515 is missing expected H atoms. Skipping. Evaluate side-chains 87 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8545 (mmp) cc_final: 0.8331 (mmp) outliers start: 1 outliers final: 1 residues processed: 87 average time/residue: 2.6021 time to fit residues: 236.0410 Evaluate side-chains 84 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.150336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.137136 restraints weight = 11566.984| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 0.99 r_work: 0.3601 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.0623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5288 Z= 0.203 Angle : 0.580 6.422 7179 Z= 0.317 Chirality : 0.044 0.169 745 Planarity : 0.005 0.042 958 Dihedral : 6.778 74.239 746 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.11 % Allowed : 13.84 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.06 (0.32), residues: 659 helix: -1.82 (0.65), residues: 47 sheet: -0.01 (0.25), residues: 351 loop : 0.56 (0.42), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 568 HIS 0.001 0.001 HIS A 649 PHE 0.017 0.002 PHE A 352 TYR 0.017 0.001 TYR A 681 ARG 0.005 0.000 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.04631 ( 280) hydrogen bonds : angle 5.99940 ( 795) SS BOND : bond 0.00023 ( 1) SS BOND : angle 0.24722 ( 2) covalent geometry : bond 0.00360 ( 5287) covalent geometry : angle 0.57983 ( 7177) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 515 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8562 (mmp) cc_final: 0.8125 (mmp) REVERT: A 377 MET cc_start: 0.7213 (OUTLIER) cc_final: 0.6535 (mpt) REVERT: A 379 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6796 (tm-30) REVERT: A 576 ARG cc_start: 0.7634 (mmp-170) cc_final: 0.7299 (mmp-170) REVERT: A 595 ARG cc_start: 0.7737 (mtm180) cc_final: 0.7401 (ttp-170) outliers start: 6 outliers final: 2 residues processed: 91 average time/residue: 2.5156 time to fit residues: 239.1856 Evaluate side-chains 86 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 404 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 54 optimal weight: 0.3980 chunk 41 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 0 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.149400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.136127 restraints weight = 11660.613| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 0.99 r_work: 0.3588 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.0754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5288 Z= 0.220 Angle : 0.582 5.967 7179 Z= 0.318 Chirality : 0.044 0.172 745 Planarity : 0.005 0.040 958 Dihedral : 6.817 74.273 746 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.66 % Allowed : 13.28 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 (0.32), residues: 659 helix: -1.75 (0.64), residues: 47 sheet: 0.02 (0.25), residues: 350 loop : 0.52 (0.42), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 568 HIS 0.001 0.001 HIS A 213 PHE 0.017 0.002 PHE A 352 TYR 0.017 0.002 TYR A 681 ARG 0.003 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.04819 ( 280) hydrogen bonds : angle 5.91642 ( 795) SS BOND : bond 0.00006 ( 1) SS BOND : angle 0.17198 ( 2) covalent geometry : bond 0.00392 ( 5287) covalent geometry : angle 0.58166 ( 7177) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 515 is missing expected H atoms. Skipping. Evaluate side-chains 95 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.823 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8605 (mmp) cc_final: 0.8195 (mmp) REVERT: A 364 ASN cc_start: 0.7744 (m110) cc_final: 0.7522 (t0) REVERT: A 377 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6503 (mpt) REVERT: A 394 MET cc_start: 0.8555 (ttt) cc_final: 0.8276 (ttt) REVERT: A 595 ARG cc_start: 0.7727 (mtm180) cc_final: 0.7396 (ttp-170) outliers start: 9 outliers final: 3 residues processed: 91 average time/residue: 2.5154 time to fit residues: 239.2090 Evaluate side-chains 86 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 404 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN A 650 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.148781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.135662 restraints weight = 11581.702| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 0.97 r_work: 0.3579 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5288 Z= 0.231 Angle : 0.590 6.686 7179 Z= 0.323 Chirality : 0.044 0.175 745 Planarity : 0.005 0.038 958 Dihedral : 6.905 75.525 746 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.29 % Allowed : 13.47 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.04 (0.32), residues: 659 helix: -1.31 (0.70), residues: 41 sheet: 0.01 (0.25), residues: 350 loop : 0.54 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 568 HIS 0.002 0.001 HIS A 213 PHE 0.017 0.002 PHE A 352 TYR 0.016 0.002 TYR A 681 ARG 0.003 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.04921 ( 280) hydrogen bonds : angle 5.92413 ( 795) SS BOND : bond 0.00018 ( 1) SS BOND : angle 0.14663 ( 2) covalent geometry : bond 0.00413 ( 5287) covalent geometry : angle 0.59029 ( 7177) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 515 is missing expected H atoms. Skipping. Evaluate side-chains 91 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8581 (mmp) cc_final: 0.8171 (mmp) REVERT: A 364 ASN cc_start: 0.7749 (m110) cc_final: 0.7507 (t0) REVERT: A 377 MET cc_start: 0.7154 (OUTLIER) cc_final: 0.6482 (mpt) REVERT: A 394 MET cc_start: 0.8552 (ttt) cc_final: 0.8307 (ttt) REVERT: A 595 ARG cc_start: 0.7696 (mtm180) cc_final: 0.7355 (ttp-170) outliers start: 7 outliers final: 3 residues processed: 87 average time/residue: 2.4532 time to fit residues: 223.2002 Evaluate side-chains 83 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 404 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 26 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 0.0770 chunk 65 optimal weight: 0.9980 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.149708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.136479 restraints weight = 11665.157| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 0.98 r_work: 0.3590 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 2.03 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5288 Z= 0.215 Angle : 0.576 6.624 7179 Z= 0.314 Chirality : 0.044 0.171 745 Planarity : 0.005 0.037 958 Dihedral : 6.846 74.737 746 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.11 % Allowed : 13.47 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.09 (0.32), residues: 659 helix: -1.63 (0.64), residues: 47 sheet: -0.03 (0.25), residues: 350 loop : 0.51 (0.42), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 568 HIS 0.002 0.001 HIS A 213 PHE 0.016 0.002 PHE A 352 TYR 0.016 0.002 TYR A 681 ARG 0.003 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.04713 ( 280) hydrogen bonds : angle 5.90417 ( 795) SS BOND : bond 0.00009 ( 1) SS BOND : angle 0.17382 ( 2) covalent geometry : bond 0.00382 ( 5287) covalent geometry : angle 0.57622 ( 7177) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 515 is missing expected H atoms. Skipping. Evaluate side-chains 88 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8591 (mmp) cc_final: 0.8236 (mmp) REVERT: A 364 ASN cc_start: 0.7660 (m110) cc_final: 0.7429 (t0) REVERT: A 595 ARG cc_start: 0.7642 (mtm180) cc_final: 0.7341 (ttp-170) REVERT: A 645 LYS cc_start: 0.8532 (mtmm) cc_final: 0.7932 (mtmp) outliers start: 6 outliers final: 3 residues processed: 85 average time/residue: 2.7623 time to fit residues: 245.3961 Evaluate side-chains 82 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 404 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 42 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 39 optimal weight: 0.0030 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.151725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.138714 restraints weight = 11627.329| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 0.97 r_work: 0.3614 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 2.01 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5288 Z= 0.181 Angle : 0.549 6.432 7179 Z= 0.298 Chirality : 0.044 0.160 745 Planarity : 0.004 0.035 958 Dihedral : 6.673 73.345 746 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.92 % Allowed : 14.21 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.10 (0.32), residues: 659 helix: -1.48 (0.66), residues: 47 sheet: -0.12 (0.25), residues: 352 loop : 0.60 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 568 HIS 0.002 0.000 HIS A 649 PHE 0.015 0.002 PHE A 352 TYR 0.015 0.001 TYR A 681 ARG 0.003 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.04253 ( 280) hydrogen bonds : angle 5.86297 ( 795) SS BOND : bond 0.00003 ( 1) SS BOND : angle 0.15749 ( 2) covalent geometry : bond 0.00320 ( 5287) covalent geometry : angle 0.54899 ( 7177) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 515 is missing expected H atoms. Skipping. Evaluate side-chains 89 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8567 (mmp) cc_final: 0.8156 (mmp) REVERT: A 364 ASN cc_start: 0.7657 (m110) cc_final: 0.7426 (t0) REVERT: A 377 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6445 (mpt) REVERT: A 379 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6718 (tm-30) REVERT: A 595 ARG cc_start: 0.7618 (mtm180) cc_final: 0.7322 (ttp-170) REVERT: A 645 LYS cc_start: 0.8502 (mtmm) cc_final: 0.7906 (mtmp) outliers start: 5 outliers final: 2 residues processed: 86 average time/residue: 2.7445 time to fit residues: 247.3048 Evaluate side-chains 83 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 404 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 22 optimal weight: 0.0870 chunk 19 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN A 160 GLN ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 ASN A 650 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.150893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.137707 restraints weight = 11715.997| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 0.99 r_work: 0.3605 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5288 Z= 0.199 Angle : 0.561 6.782 7179 Z= 0.305 Chirality : 0.044 0.166 745 Planarity : 0.005 0.037 958 Dihedral : 6.738 73.771 746 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.11 % Allowed : 13.47 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.09 (0.32), residues: 659 helix: -1.57 (0.65), residues: 47 sheet: -0.08 (0.25), residues: 352 loop : 0.59 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 568 HIS 0.002 0.001 HIS A 649 PHE 0.016 0.002 PHE A 352 TYR 0.015 0.001 TYR A 681 ARG 0.004 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.04494 ( 280) hydrogen bonds : angle 5.85115 ( 795) SS BOND : bond 0.00047 ( 1) SS BOND : angle 0.11447 ( 2) covalent geometry : bond 0.00353 ( 5287) covalent geometry : angle 0.56128 ( 7177) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 515 is missing expected H atoms. Skipping. Evaluate side-chains 87 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8593 (mmp) cc_final: 0.8153 (mmp) REVERT: A 364 ASN cc_start: 0.7669 (m110) cc_final: 0.7469 (t0) REVERT: A 377 MET cc_start: 0.7080 (OUTLIER) cc_final: 0.6443 (mpt) REVERT: A 595 ARG cc_start: 0.7645 (mtm180) cc_final: 0.7353 (ttp-170) REVERT: A 645 LYS cc_start: 0.8516 (mtmm) cc_final: 0.7924 (mtmp) outliers start: 6 outliers final: 3 residues processed: 83 average time/residue: 2.8812 time to fit residues: 251.2376 Evaluate side-chains 83 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 404 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 17 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 ASN A 650 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.147623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.134578 restraints weight = 11635.835| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 0.96 r_work: 0.3577 rms_B_bonded: 1.13 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 1.98 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 5288 Z= 0.263 Angle : 0.616 7.158 7179 Z= 0.337 Chirality : 0.043 0.187 745 Planarity : 0.005 0.043 958 Dihedral : 7.026 75.484 746 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.92 % Allowed : 14.21 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.01 (0.32), residues: 659 helix: -1.76 (0.63), residues: 47 sheet: 0.10 (0.26), residues: 345 loop : 0.50 (0.42), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 568 HIS 0.002 0.001 HIS A 342 PHE 0.018 0.003 PHE A 352 TYR 0.016 0.002 TYR A 681 ARG 0.004 0.001 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.05302 ( 280) hydrogen bonds : angle 5.93810 ( 795) SS BOND : bond 0.00069 ( 1) SS BOND : angle 0.20570 ( 2) covalent geometry : bond 0.00475 ( 5287) covalent geometry : angle 0.61562 ( 7177) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 515 is missing expected H atoms. Skipping. Evaluate side-chains 85 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.780 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8675 (mmp) cc_final: 0.8234 (mmp) REVERT: A 377 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.6530 (mpt) REVERT: A 595 ARG cc_start: 0.7673 (mtm180) cc_final: 0.7385 (ttp-170) outliers start: 5 outliers final: 3 residues processed: 82 average time/residue: 2.9555 time to fit residues: 252.3413 Evaluate side-chains 84 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 404 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 0 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 49 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 GLN ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 ASN A 650 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.152156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.139258 restraints weight = 11612.263| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 0.96 r_work: 0.3630 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 2.01 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5288 Z= 0.174 Angle : 0.550 6.610 7179 Z= 0.298 Chirality : 0.044 0.155 745 Planarity : 0.004 0.038 958 Dihedral : 6.668 72.041 746 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.92 % Allowed : 14.02 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.10 (0.33), residues: 659 helix: -1.56 (0.66), residues: 47 sheet: -0.10 (0.26), residues: 352 loop : 0.59 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 568 HIS 0.003 0.001 HIS A 649 PHE 0.014 0.002 PHE A 352 TYR 0.014 0.001 TYR A 681 ARG 0.004 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.04151 ( 280) hydrogen bonds : angle 5.90451 ( 795) SS BOND : bond 0.00033 ( 1) SS BOND : angle 0.09887 ( 2) covalent geometry : bond 0.00311 ( 5287) covalent geometry : angle 0.55028 ( 7177) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 515 is missing expected H atoms. Skipping. Evaluate side-chains 87 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.754 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8604 (mmp) cc_final: 0.8270 (mmp) REVERT: A 377 MET cc_start: 0.7133 (OUTLIER) cc_final: 0.6484 (mpt) REVERT: A 595 ARG cc_start: 0.7651 (mtm180) cc_final: 0.7381 (ttp-170) REVERT: A 645 LYS cc_start: 0.8512 (mtmm) cc_final: 0.7926 (mtmp) outliers start: 5 outliers final: 3 residues processed: 84 average time/residue: 2.5042 time to fit residues: 219.7265 Evaluate side-chains 85 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 404 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 578 ASN A 650 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.147797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.134709 restraints weight = 11523.970| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 0.96 r_work: 0.3578 rms_B_bonded: 1.13 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 1.98 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 5288 Z= 0.266 Angle : 0.619 7.269 7179 Z= 0.338 Chirality : 0.044 0.189 745 Planarity : 0.006 0.045 958 Dihedral : 7.037 75.388 746 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.74 % Allowed : 14.02 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.00 (0.32), residues: 659 helix: -1.80 (0.62), residues: 47 sheet: 0.08 (0.26), residues: 345 loop : 0.51 (0.42), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 568 HIS 0.003 0.001 HIS A 649 PHE 0.018 0.003 PHE A 352 TYR 0.017 0.002 TYR A 681 ARG 0.004 0.001 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.05327 ( 280) hydrogen bonds : angle 5.95502 ( 795) SS BOND : bond 0.00065 ( 1) SS BOND : angle 0.24306 ( 2) covalent geometry : bond 0.00483 ( 5287) covalent geometry : angle 0.61858 ( 7177) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 515 is missing expected H atoms. Skipping. Evaluate side-chains 84 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8682 (mmp) cc_final: 0.8235 (mmp) REVERT: A 377 MET cc_start: 0.7195 (OUTLIER) cc_final: 0.6515 (mpt) REVERT: A 595 ARG cc_start: 0.7668 (mtm180) cc_final: 0.7377 (ttp-170) outliers start: 4 outliers final: 3 residues processed: 82 average time/residue: 2.7940 time to fit residues: 238.5355 Evaluate side-chains 85 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 404 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 7 optimal weight: 0.2980 chunk 38 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 GLN A 650 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.152001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.139064 restraints weight = 11558.410| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 0.96 r_work: 0.3630 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5288 Z= 0.175 Angle : 0.554 6.716 7179 Z= 0.300 Chirality : 0.044 0.157 745 Planarity : 0.004 0.037 958 Dihedral : 6.687 71.777 746 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.92 % Allowed : 13.84 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.09 (0.33), residues: 659 helix: -1.56 (0.66), residues: 47 sheet: -0.10 (0.26), residues: 352 loop : 0.60 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 568 HIS 0.004 0.001 HIS A 649 PHE 0.014 0.002 PHE A 352 TYR 0.014 0.001 TYR A 681 ARG 0.004 0.001 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.04179 ( 280) hydrogen bonds : angle 5.90631 ( 795) SS BOND : bond 0.00004 ( 1) SS BOND : angle 0.10881 ( 2) covalent geometry : bond 0.00314 ( 5287) covalent geometry : angle 0.55393 ( 7177) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9349.05 seconds wall clock time: 161 minutes 58.49 seconds (9718.49 seconds total)