Starting phenix.real_space_refine on Sat Nov 16 02:48:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c4o_45192/11_2024/9c4o_45192_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c4o_45192/11_2024/9c4o_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c4o_45192/11_2024/9c4o_45192.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c4o_45192/11_2024/9c4o_45192.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c4o_45192/11_2024/9c4o_45192_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c4o_45192/11_2024/9c4o_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-5513/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: 9.31, per 1000 atoms: 0.92 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: 3.90 Conformation dependent library (CDL) restraints added in 776.9 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: 0.80 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: 4.22 Time building geometry restraints manager: 4.55 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: 3.030 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: 0.220 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 33.370 Find NCS groups from input model: 0.280 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:13.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.250 ------------------------------------------------------------------------------- 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 5287 Z= 0.277 Angle : 0.647 6.461 7177 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 *********************** 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 : 0.817 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: 2.7194 time to fit residues: 246.6375 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 : 0.864 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 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 5287 Z= 0.238 Angle : 0.580 6.422 7177 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 *********************** 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 : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8598 (mmp) cc_final: 0.8172 (mmp) REVERT: A 377 MET cc_start: 0.7191 (OUTLIER) cc_final: 0.6517 (mpt) REVERT: A 379 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6830 (tm-30) REVERT: A 576 ARG cc_start: 0.7732 (mmp-170) cc_final: 0.7396 (mmp-170) REVERT: A 595 ARG cc_start: 0.7741 (mtm180) cc_final: 0.7411 (ttp-170) outliers start: 6 outliers final: 2 residues processed: 91 average time/residue: 2.6073 time to fit residues: 247.6236 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 : 0.946 ------------------------------------------------------------------------------- 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 33 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.0726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 5287 Z= 0.321 Angle : 0.626 6.321 7177 Z= 0.344 Chirality : 0.044 0.189 745 Planarity : 0.005 0.042 958 Dihedral : 7.056 75.124 746 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.48 % Allowed : 13.65 % 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: 0.02 (0.32), residues: 659 helix: -1.84 (0.63), residues: 47 sheet: 0.14 (0.26), residues: 345 loop : 0.46 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 568 HIS 0.002 0.001 HIS A 342 PHE 0.018 0.003 PHE A 352 TYR 0.018 0.002 TYR A 681 ARG 0.003 0.001 ARG A 658 *********************** 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 93 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8665 (mmp) cc_final: 0.8237 (mmp) REVERT: A 377 MET cc_start: 0.7164 (OUTLIER) cc_final: 0.6496 (mpt) REVERT: A 595 ARG cc_start: 0.7750 (mtm180) cc_final: 0.7429 (ttp-170) outliers start: 8 outliers final: 3 residues processed: 88 average time/residue: 2.7563 time to fit residues: 252.8357 Evaluate side-chains 87 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 59 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN A 650 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.0803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 5287 Z= 0.307 Angle : 0.617 6.942 7177 Z= 0.338 Chirality : 0.044 0.183 745 Planarity : 0.005 0.041 958 Dihedral : 7.069 75.550 746 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.11 % Allowed : 13.65 % 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: 0.03 (0.32), residues: 659 helix: -1.81 (0.62), residues: 47 sheet: 0.16 (0.26), residues: 345 loop : 0.43 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 568 HIS 0.002 0.001 HIS A 342 PHE 0.017 0.003 PHE A 352 TYR 0.018 0.002 TYR A 681 ARG 0.003 0.000 ARG A 287 *********************** 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 88 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8670 (mmp) cc_final: 0.8262 (mmp) REVERT: A 377 MET cc_start: 0.7103 (OUTLIER) cc_final: 0.6440 (mpt) REVERT: A 595 ARG cc_start: 0.7730 (mtm180) cc_final: 0.7412 (ttp-170) outliers start: 6 outliers final: 3 residues processed: 85 average time/residue: 2.7577 time to fit residues: 244.3627 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 : 1.164 ------------------------------------------------------------------------------- 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 36 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5287 Z= 0.301 Angle : 0.613 7.071 7177 Z= 0.336 Chirality : 0.044 0.182 745 Planarity : 0.005 0.040 958 Dihedral : 7.069 74.843 746 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % 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: 0.02 (0.32), residues: 659 helix: -1.77 (0.63), residues: 47 sheet: 0.15 (0.26), residues: 345 loop : 0.43 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 568 HIS 0.002 0.001 HIS A 342 PHE 0.018 0.002 PHE A 352 TYR 0.017 0.002 TYR A 681 ARG 0.003 0.000 ARG A 287 *********************** 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 86 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8663 (mmp) cc_final: 0.8306 (mmp) REVERT: A 377 MET cc_start: 0.7104 (OUTLIER) cc_final: 0.6314 (mpt) REVERT: A 595 ARG cc_start: 0.7709 (mtm180) cc_final: 0.7392 (ttp-170) REVERT: A 645 LYS cc_start: 0.8558 (mtmm) cc_final: 0.7967 (mtmp) outliers start: 5 outliers final: 3 residues processed: 83 average time/residue: 2.7932 time to fit residues: 241.4360 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 : 0.825 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 21 optimal weight: 0.0980 chunk 33 optimal weight: 0.4980 chunk 61 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 650 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5287 Z= 0.193 Angle : 0.543 6.404 7177 Z= 0.295 Chirality : 0.044 0.153 745 Planarity : 0.004 0.036 958 Dihedral : 6.639 71.221 746 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.92 % Allowed : 13.47 % Favored : 85.61 % 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: -0.02 (0.33), residues: 659 helix: -1.10 (0.73), residues: 41 sheet: -0.10 (0.26), residues: 352 loop : 0.60 (0.41), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 568 HIS 0.002 0.000 HIS A 649 PHE 0.014 0.002 PHE A 352 TYR 0.015 0.001 TYR A 681 ARG 0.004 0.000 ARG A 96 *********************** 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 93 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.730 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8619 (mmp) cc_final: 0.8212 (mmp) REVERT: A 379 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6707 (tm-30) REVERT: A 595 ARG cc_start: 0.7670 (mtm180) cc_final: 0.7384 (ttp-170) REVERT: A 645 LYS cc_start: 0.8520 (mtmm) cc_final: 0.7928 (mtmp) outliers start: 5 outliers final: 2 residues processed: 90 average time/residue: 2.6790 time to fit residues: 253.2028 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 : 0.843 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 GLN A 578 ASN A 650 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5287 Z= 0.272 Angle : 0.588 6.959 7177 Z= 0.321 Chirality : 0.044 0.178 745 Planarity : 0.005 0.039 958 Dihedral : 6.885 73.356 746 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.67 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: -0.00 (0.33), residues: 659 helix: -1.59 (0.65), residues: 47 sheet: 0.05 (0.26), residues: 345 loop : 0.52 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 568 HIS 0.002 0.001 HIS A 649 PHE 0.017 0.002 PHE A 352 TYR 0.016 0.002 TYR A 681 ARG 0.003 0.000 ARG A 287 *********************** 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 : 0.869 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8657 (mmp) cc_final: 0.8226 (mmp) REVERT: A 377 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.6425 (mpt) REVERT: A 595 ARG cc_start: 0.7672 (mtm180) cc_final: 0.7377 (ttp-170) REVERT: A 645 LYS cc_start: 0.8555 (mtmm) cc_final: 0.7962 (mtmp) outliers start: 6 outliers final: 3 residues processed: 83 average time/residue: 2.7385 time to fit residues: 237.0627 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 : 0.796 ------------------------------------------------------------------------------- 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 12 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 GLN A 578 ASN A 650 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5287 Z= 0.258 Angle : 0.583 7.128 7177 Z= 0.317 Chirality : 0.044 0.171 745 Planarity : 0.005 0.039 958 Dihedral : 6.860 72.847 746 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.74 % Allowed : 13.65 % Favored : 85.61 % 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: -0.08 (0.32), residues: 659 helix: -1.65 (0.64), residues: 47 sheet: 0.00 (0.26), residues: 350 loop : 0.46 (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 649 PHE 0.017 0.002 PHE A 352 TYR 0.016 0.002 TYR A 681 ARG 0.004 0.000 ARG A 287 *********************** 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: 4 poor density : 81 time to evaluate : 0.747 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8656 (mmp) cc_final: 0.8221 (mmp) REVERT: A 377 MET cc_start: 0.7071 (OUTLIER) cc_final: 0.6423 (mpt) REVERT: A 595 ARG cc_start: 0.7671 (mtm180) cc_final: 0.7375 (ttp-170) REVERT: A 645 LYS cc_start: 0.8558 (mtmm) cc_final: 0.7968 (mtmp) outliers start: 4 outliers final: 3 residues processed: 83 average time/residue: 2.7155 time to fit residues: 235.2285 Evaluate side-chains 82 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 25 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 GLN A 578 ASN A 650 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5287 Z= 0.288 Angle : 0.603 7.282 7177 Z= 0.329 Chirality : 0.044 0.181 745 Planarity : 0.005 0.040 958 Dihedral : 6.972 73.662 746 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % 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: -0.01 (0.32), residues: 659 helix: -1.71 (0.64), residues: 47 sheet: 0.08 (0.26), residues: 345 loop : 0.47 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 568 HIS 0.002 0.001 HIS A 649 PHE 0.018 0.002 PHE A 352 TYR 0.016 0.002 TYR A 681 ARG 0.004 0.000 ARG A 287 *********************** 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 86 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.803 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8668 (mmp) cc_final: 0.8225 (mmp) REVERT: A 377 MET cc_start: 0.7104 (OUTLIER) cc_final: 0.6429 (mpt) REVERT: A 595 ARG cc_start: 0.7662 (mtm180) cc_final: 0.7362 (ttp-170) REVERT: A 645 LYS cc_start: 0.8573 (mtmm) cc_final: 0.7981 (mtmp) outliers start: 5 outliers final: 3 residues processed: 83 average time/residue: 2.8735 time to fit residues: 248.2304 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 : 0.797 ------------------------------------------------------------------------------- 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 60 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 GLN A 556 GLN A 578 ASN A 650 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5287 Z= 0.225 Angle : 0.565 6.767 7177 Z= 0.307 Chirality : 0.044 0.162 745 Planarity : 0.004 0.038 958 Dihedral : 6.747 71.050 746 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % 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: -0.11 (0.33), residues: 659 helix: -1.59 (0.65), residues: 47 sheet: -0.05 (0.26), residues: 350 loop : 0.49 (0.42), residues: 262 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 0.015 0.002 PHE A 352 TYR 0.015 0.001 TYR A 681 ARG 0.004 0.000 ARG A 287 ********************** 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: 5 poor density : 79 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8639 (mmp) cc_final: 0.8198 (mmp) REVERT: A 377 MET cc_start: 0.7074 (OUTLIER) cc_final: 0.6415 (mpt) REVERT: A 595 ARG cc_start: 0.7655 (mtm180) cc_final: 0.7369 (ttp-170) REVERT: A 645 LYS cc_start: 0.8544 (mtmm) cc_final: 0.7954 (mtmp) outliers start: 5 outliers final: 3 residues processed: 81 average time/residue: 2.6776 time to fit residues: 227.4229 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 : 0.726 ------------------------------------------------------------------------------- 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 52 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 6 optimal weight: 0.0980 chunk 9 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 650 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.148617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.135629 restraints weight = 11406.200| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 0.95 r_work: 0.3590 rms_B_bonded: 1.12 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 1.97 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5287 Z= 0.288 Angle : 0.606 7.202 7177 Z= 0.330 Chirality : 0.044 0.182 745 Planarity : 0.005 0.040 958 Dihedral : 6.976 73.300 746 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % 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: -0.02 (0.33), residues: 659 helix: -1.72 (0.64), residues: 47 sheet: 0.06 (0.26), residues: 345 loop : 0.49 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 568 HIS 0.004 0.001 HIS A 649 PHE 0.018 0.002 PHE A 352 TYR 0.016 0.002 TYR A 681 ARG 0.004 0.000 ARG A 287 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5287.61 seconds wall clock time: 94 minutes 15.66 seconds (5655.66 seconds total)