Starting phenix.real_space_refine on Fri Dec 27 07:09:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y6n_33644/12_2024/7y6n_33644.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y6n_33644/12_2024/7y6n_33644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y6n_33644/12_2024/7y6n_33644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y6n_33644/12_2024/7y6n_33644.map" model { file = "/net/cci-nas-00/data/ceres_data/7y6n_33644/12_2024/7y6n_33644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y6n_33644/12_2024/7y6n_33644.cif" } resolution = 4.4 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2112 2.51 5 N 565 2.21 5 O 635 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3327 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1568 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 11, 'TRANS': 186} Chain: "H" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 948 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 797 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.52, per 1000 atoms: 0.76 Number of scatterers: 3327 At special positions: 0 Unit cell: (65.491, 60.517, 107.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 635 8.00 N 565 7.00 C 2112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 480.8 milliseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 778 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 6 sheets defined 9.9% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.916A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.965A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.909A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.933A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.496A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY H 50 " --> pdb=" O ALA H 59 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA H 59 " --> pdb=" O GLY H 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.500A pdb=" N LEU L 11 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) 100 hydrogen bonds defined for protein. 228 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.67 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1069 1.34 - 1.47: 901 1.47 - 1.59: 1424 1.59 - 1.71: 0 1.71 - 1.83: 17 Bond restraints: 3411 Sorted by residual: bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.13e+00 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.35e+00 bond pdb=" CB LYS A 462 " pdb=" CG LYS A 462 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.10e+00 bond pdb=" N ASN H 77 " pdb=" CA ASN H 77 " ideal model delta sigma weight residual 1.457 1.471 -0.013 1.29e-02 6.01e+03 1.07e+00 bond pdb=" C3 NAG A1301 " pdb=" O3 NAG A1301 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 1.03e+00 ... (remaining 3406 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 4365 1.54 - 3.09: 214 3.09 - 4.63: 38 4.63 - 6.18: 10 6.18 - 7.72: 8 Bond angle restraints: 4635 Sorted by residual: angle pdb=" C PRO A 479 " pdb=" N CYS A 480 " pdb=" CA CYS A 480 " ideal model delta sigma weight residual 121.94 114.95 6.99 2.00e+00 2.50e-01 1.22e+01 angle pdb=" N PHE A 338 " pdb=" CA PHE A 338 " pdb=" C PHE A 338 " ideal model delta sigma weight residual 114.56 110.18 4.38 1.27e+00 6.20e-01 1.19e+01 angle pdb=" CB LYS A 462 " pdb=" CG LYS A 462 " pdb=" CD LYS A 462 " ideal model delta sigma weight residual 111.30 118.99 -7.69 2.30e+00 1.89e-01 1.12e+01 angle pdb=" N GLY L 41 " pdb=" CA GLY L 41 " pdb=" C GLY L 41 " ideal model delta sigma weight residual 113.58 116.85 -3.27 1.07e+00 8.73e-01 9.33e+00 angle pdb=" N PHE L 92 " pdb=" CA PHE L 92 " pdb=" C PHE L 92 " ideal model delta sigma weight residual 109.96 105.46 4.50 1.58e+00 4.01e-01 8.10e+00 ... (remaining 4630 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.24: 1799 16.24 - 32.47: 176 32.47 - 48.71: 30 48.71 - 64.94: 14 64.94 - 81.18: 3 Dihedral angle restraints: 2022 sinusoidal: 796 harmonic: 1226 Sorted by residual: dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 11.82 81.18 1 1.00e+01 1.00e-02 8.13e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 155.64 -62.64 1 1.00e+01 1.00e-02 5.19e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -147.95 61.95 1 1.00e+01 1.00e-02 5.09e+01 ... (remaining 2019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 356 0.046 - 0.091: 106 0.091 - 0.137: 34 0.137 - 0.182: 4 0.182 - 0.228: 1 Chirality restraints: 501 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA THR L 94 " pdb=" N THR L 94 " pdb=" C THR L 94 " pdb=" CB THR L 94 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.46e-01 chirality pdb=" CA ILE A 434 " pdb=" N ILE A 434 " pdb=" C ILE A 434 " pdb=" CB ILE A 434 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.78e-01 ... (remaining 498 not shown) Planarity restraints: 602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 490 " 0.070 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO A 491 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO A 491 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 491 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 36 " -0.012 2.00e-02 2.50e+03 9.63e-03 2.32e+00 pdb=" CG TRP H 36 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP H 36 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP H 36 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 36 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP H 36 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP H 36 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 36 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 36 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP H 36 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL L 58 " -0.022 5.00e-02 4.00e+02 3.32e-02 1.76e+00 pdb=" N PRO L 59 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO L 59 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO L 59 " -0.018 5.00e-02 4.00e+02 ... (remaining 599 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 507 2.76 - 3.29: 3418 3.29 - 3.83: 5417 3.83 - 4.36: 6147 4.36 - 4.90: 10455 Nonbonded interactions: 25944 Sorted by model distance: nonbonded pdb=" O GLY H 85 " pdb=" NH1 ARG H 87 " model vdw 2.222 3.120 nonbonded pdb=" OG SER L 14 " pdb=" O LYS L 107 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR H 102 " pdb=" NE2 GLN L 55 " model vdw 2.266 3.120 nonbonded pdb=" O PRO L 8 " pdb=" OG1 THR L 102 " model vdw 2.269 3.040 nonbonded pdb=" OD1 ASN A 354 " pdb=" N ARG A 355 " model vdw 2.302 3.120 ... (remaining 25939 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.770 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5575 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3411 Z= 0.215 Angle : 0.837 7.724 4635 Z= 0.442 Chirality : 0.047 0.228 501 Planarity : 0.006 0.108 601 Dihedral : 12.983 81.022 1226 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.14 % Favored : 87.86 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.77 (0.39), residues: 420 helix: -2.48 (0.92), residues: 28 sheet: -1.35 (0.43), residues: 138 loop : -2.10 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 36 HIS 0.003 0.001 HIS H 35 PHE 0.021 0.001 PHE L 92 TYR 0.009 0.001 TYR A 365 ARG 0.003 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 387 LEU cc_start: 0.5807 (tt) cc_final: 0.5411 (tp) REVERT: A 417 LYS cc_start: 0.6909 (ptmt) cc_final: 0.6335 (tppt) REVERT: A 424 LYS cc_start: 0.7203 (tmmt) cc_final: 0.6589 (tptt) REVERT: A 436 TRP cc_start: 0.6532 (p90) cc_final: 0.5933 (p90) REVERT: A 439 ASN cc_start: 0.6843 (t0) cc_final: 0.6558 (t0) REVERT: A 453 TYR cc_start: 0.6462 (p90) cc_final: 0.5882 (p90) REVERT: A 461 LEU cc_start: 0.6388 (mm) cc_final: 0.6047 (mm) REVERT: A 466 ARG cc_start: 0.7581 (mtp85) cc_final: 0.7368 (ttm170) REVERT: A 489 TYR cc_start: 0.7858 (m-10) cc_final: 0.7087 (m-10) REVERT: H 78 SER cc_start: 0.7214 (t) cc_final: 0.6535 (m) REVERT: H 90 ASP cc_start: 0.4947 (m-30) cc_final: 0.4626 (m-30) REVERT: H 101 ARG cc_start: 0.7298 (tpt170) cc_final: 0.5685 (ttm170) REVERT: L 92 PHE cc_start: 0.5994 (t80) cc_final: 0.5333 (t80) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1702 time to fit residues: 21.6711 Evaluate side-chains 77 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 20.0000 chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 10 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 0.0770 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 20.0000 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 overall best weight: 1.8742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5639 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3411 Z= 0.210 Angle : 0.741 6.281 4635 Z= 0.382 Chirality : 0.047 0.189 501 Planarity : 0.006 0.072 601 Dihedral : 5.948 25.480 491 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.64 (0.40), residues: 420 helix: -2.06 (0.98), residues: 27 sheet: -1.55 (0.40), residues: 150 loop : -1.86 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 35 HIS 0.003 0.002 HIS H 35 PHE 0.014 0.002 PHE A 497 TYR 0.011 0.002 TYR L 49 ARG 0.004 0.001 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 387 LEU cc_start: 0.5775 (tt) cc_final: 0.5406 (tp) REVERT: A 417 LYS cc_start: 0.7148 (ptmt) cc_final: 0.6539 (tppt) REVERT: A 424 LYS cc_start: 0.7387 (tmmt) cc_final: 0.7095 (tptt) REVERT: A 436 TRP cc_start: 0.6594 (p90) cc_final: 0.5978 (p90) REVERT: A 453 TYR cc_start: 0.6519 (p90) cc_final: 0.5873 (p90) REVERT: A 461 LEU cc_start: 0.6456 (mm) cc_final: 0.6208 (mm) REVERT: H 34 MET cc_start: 0.6959 (tpt) cc_final: 0.6632 (tpt) REVERT: H 78 SER cc_start: 0.7411 (t) cc_final: 0.6836 (m) REVERT: H 101 ARG cc_start: 0.7299 (tpt170) cc_final: 0.5616 (ttm170) REVERT: L 22 THR cc_start: 0.6442 (p) cc_final: 0.6200 (m) REVERT: L 92 PHE cc_start: 0.6327 (t80) cc_final: 0.5518 (t80) REVERT: L 102 THR cc_start: 0.5498 (t) cc_final: 0.5093 (m) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1609 time to fit residues: 16.6504 Evaluate side-chains 72 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5607 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3411 Z= 0.166 Angle : 0.691 6.705 4635 Z= 0.353 Chirality : 0.046 0.192 501 Planarity : 0.004 0.034 601 Dihedral : 5.587 23.994 491 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.14 % Favored : 87.86 % Rotamer: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.63 (0.40), residues: 420 helix: -2.19 (0.98), residues: 27 sheet: -1.57 (0.40), residues: 151 loop : -1.81 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 35 HIS 0.002 0.001 HIS H 35 PHE 0.012 0.001 PHE A 497 TYR 0.010 0.001 TYR A 453 ARG 0.004 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 387 LEU cc_start: 0.6023 (tt) cc_final: 0.5662 (tp) REVERT: A 417 LYS cc_start: 0.7172 (ptmt) cc_final: 0.6572 (tppt) REVERT: A 424 LYS cc_start: 0.7271 (tmmt) cc_final: 0.6881 (tptp) REVERT: A 436 TRP cc_start: 0.6658 (p90) cc_final: 0.6046 (p90) REVERT: A 453 TYR cc_start: 0.6585 (p90) cc_final: 0.6127 (p90) REVERT: A 461 LEU cc_start: 0.6512 (mm) cc_final: 0.6248 (mm) REVERT: H 78 SER cc_start: 0.7335 (t) cc_final: 0.6895 (m) REVERT: H 93 LEU cc_start: 0.6275 (mt) cc_final: 0.6011 (mt) REVERT: H 101 ARG cc_start: 0.7204 (tpt170) cc_final: 0.5345 (ttm170) REVERT: L 92 PHE cc_start: 0.6175 (t80) cc_final: 0.5373 (t80) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1430 time to fit residues: 14.1879 Evaluate side-chains 69 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN A 474 GLN L 34 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5699 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 3411 Z= 0.328 Angle : 0.879 7.605 4635 Z= 0.457 Chirality : 0.052 0.247 501 Planarity : 0.006 0.039 601 Dihedral : 7.613 45.363 491 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.86 % Favored : 87.14 % Rotamer: Outliers : 0.28 % Allowed : 4.44 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.79 (0.41), residues: 420 helix: -2.46 (0.94), residues: 27 sheet: -1.75 (0.39), residues: 148 loop : -1.84 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP L 35 HIS 0.004 0.002 HIS H 35 PHE 0.014 0.002 PHE A 497 TYR 0.020 0.003 TYR A 380 ARG 0.004 0.001 ARG H 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 408 ARG cc_start: 0.7194 (ppt170) cc_final: 0.6980 (ptm-80) REVERT: A 417 LYS cc_start: 0.7325 (ptmt) cc_final: 0.6762 (tppt) REVERT: A 424 LYS cc_start: 0.6852 (tmmt) cc_final: 0.6449 (tptt) REVERT: A 429 PHE cc_start: 0.6510 (t80) cc_final: 0.6203 (t80) REVERT: A 461 LEU cc_start: 0.6413 (mm) cc_final: 0.5988 (mm) REVERT: A 462 LYS cc_start: 0.8490 (tppt) cc_final: 0.7507 (ptmt) REVERT: A 515 PHE cc_start: 0.6814 (m-10) cc_final: 0.6601 (m-10) REVERT: H 13 GLN cc_start: 0.7007 (mm-40) cc_final: 0.6208 (pm20) REVERT: H 72 ARG cc_start: 0.5616 (tpt-90) cc_final: 0.5375 (tpt-90) REVERT: H 78 SER cc_start: 0.7444 (t) cc_final: 0.7130 (m) REVERT: H 90 ASP cc_start: 0.5207 (m-30) cc_final: 0.4843 (m-30) REVERT: H 93 LEU cc_start: 0.6017 (mt) cc_final: 0.5768 (mt) REVERT: H 122 VAL cc_start: 0.3821 (t) cc_final: 0.3417 (t) REVERT: L 62 PHE cc_start: 0.6027 (m-80) cc_final: 0.5682 (m-80) REVERT: L 92 PHE cc_start: 0.6342 (t80) cc_final: 0.5494 (t80) REVERT: L 102 THR cc_start: 0.5210 (t) cc_final: 0.4775 (m) outliers start: 1 outliers final: 0 residues processed: 89 average time/residue: 0.1787 time to fit residues: 19.0883 Evaluate side-chains 72 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 16 optimal weight: 0.0170 chunk 33 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 overall best weight: 2.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5675 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3411 Z= 0.225 Angle : 0.780 7.720 4635 Z= 0.399 Chirality : 0.048 0.171 501 Planarity : 0.005 0.034 601 Dihedral : 6.598 31.993 491 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.10 % Favored : 86.90 % Rotamer: Outliers : 0.28 % Allowed : 1.94 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.80 (0.42), residues: 420 helix: -2.60 (0.94), residues: 27 sheet: -1.71 (0.40), residues: 149 loop : -1.86 (0.43), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 35 HIS 0.001 0.001 HIS H 35 PHE 0.013 0.002 PHE A 497 TYR 0.015 0.002 TYR A 453 ARG 0.003 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 408 ARG cc_start: 0.7286 (ppt170) cc_final: 0.6984 (ptm-80) REVERT: A 417 LYS cc_start: 0.7287 (ptmt) cc_final: 0.6781 (tppt) REVERT: A 424 LYS cc_start: 0.6981 (tmmt) cc_final: 0.6437 (tptp) REVERT: A 429 PHE cc_start: 0.6274 (t80) cc_final: 0.5890 (t80) REVERT: A 461 LEU cc_start: 0.6425 (mm) cc_final: 0.6125 (mm) REVERT: A 462 LYS cc_start: 0.8487 (tppt) cc_final: 0.7561 (ptmt) REVERT: H 13 GLN cc_start: 0.7036 (mm-40) cc_final: 0.6209 (pm20) REVERT: H 72 ARG cc_start: 0.5501 (tpt-90) cc_final: 0.4822 (tpt-90) REVERT: H 93 LEU cc_start: 0.6072 (mt) cc_final: 0.5855 (mt) REVERT: H 113 PHE cc_start: 0.6883 (m-80) cc_final: 0.6673 (m-80) REVERT: H 122 VAL cc_start: 0.4076 (t) cc_final: 0.3741 (t) REVERT: L 62 PHE cc_start: 0.6085 (m-80) cc_final: 0.5752 (m-80) REVERT: L 92 PHE cc_start: 0.6059 (t80) cc_final: 0.5152 (t80) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.2050 time to fit residues: 20.8652 Evaluate side-chains 73 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 32 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 0.1980 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN L 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5650 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3411 Z= 0.178 Angle : 0.721 8.253 4635 Z= 0.369 Chirality : 0.046 0.188 501 Planarity : 0.005 0.034 601 Dihedral : 6.008 25.579 491 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.86 % Favored : 87.14 % Rotamer: Outliers : 0.28 % Allowed : 3.06 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.58 (0.42), residues: 420 helix: -2.44 (0.99), residues: 27 sheet: -1.44 (0.41), residues: 145 loop : -1.81 (0.43), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 114 HIS 0.001 0.001 HIS H 35 PHE 0.017 0.002 PHE L 98 TYR 0.013 0.001 TYR A 453 ARG 0.002 0.000 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 393 THR cc_start: 0.6686 (m) cc_final: 0.6145 (p) REVERT: A 408 ARG cc_start: 0.7241 (ppt170) cc_final: 0.6954 (ptm-80) REVERT: A 417 LYS cc_start: 0.7202 (ptmt) cc_final: 0.6800 (tppt) REVERT: A 424 LYS cc_start: 0.7136 (tmmt) cc_final: 0.6690 (tptp) REVERT: A 439 ASN cc_start: 0.6546 (OUTLIER) cc_final: 0.6172 (t0) REVERT: A 461 LEU cc_start: 0.6303 (mm) cc_final: 0.5855 (mm) REVERT: A 462 LYS cc_start: 0.8602 (tppt) cc_final: 0.7756 (pttm) REVERT: A 515 PHE cc_start: 0.6731 (m-10) cc_final: 0.6516 (m-10) REVERT: H 13 GLN cc_start: 0.7070 (mm-40) cc_final: 0.6201 (pm20) REVERT: H 122 VAL cc_start: 0.4015 (t) cc_final: 0.3614 (t) REVERT: L 62 PHE cc_start: 0.6152 (m-80) cc_final: 0.5814 (m-80) REVERT: L 92 PHE cc_start: 0.6091 (t80) cc_final: 0.5119 (t80) outliers start: 1 outliers final: 0 residues processed: 82 average time/residue: 0.1891 time to fit residues: 18.5804 Evaluate side-chains 72 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN L 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5668 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3411 Z= 0.255 Angle : 0.797 8.298 4635 Z= 0.410 Chirality : 0.048 0.175 501 Planarity : 0.005 0.052 601 Dihedral : 6.636 28.466 491 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.57 % Favored : 86.43 % Rotamer: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.73 (0.42), residues: 420 helix: -2.36 (0.99), residues: 27 sheet: -1.66 (0.41), residues: 148 loop : -1.84 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 35 HIS 0.002 0.001 HIS H 35 PHE 0.016 0.002 PHE A 456 TYR 0.017 0.002 TYR A 453 ARG 0.007 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.380 Fit side-chains REVERT: A 408 ARG cc_start: 0.7256 (ppt170) cc_final: 0.6921 (ptm-80) REVERT: A 417 LYS cc_start: 0.7311 (ptmt) cc_final: 0.6876 (tppt) REVERT: A 424 LYS cc_start: 0.7011 (tmmt) cc_final: 0.6660 (tptt) REVERT: A 439 ASN cc_start: 0.7317 (t0) cc_final: 0.6957 (t0) REVERT: A 461 LEU cc_start: 0.6273 (mm) cc_final: 0.5954 (mm) REVERT: A 462 LYS cc_start: 0.8614 (tppt) cc_final: 0.7752 (pttm) REVERT: H 13 GLN cc_start: 0.6971 (mm-40) cc_final: 0.6166 (pm20) REVERT: H 72 ARG cc_start: 0.5374 (tpt-90) cc_final: 0.4923 (tpt-90) REVERT: H 90 ASP cc_start: 0.5743 (m-30) cc_final: 0.5511 (m-30) REVERT: H 101 ARG cc_start: 0.7455 (tpt170) cc_final: 0.6120 (ptp-170) REVERT: H 122 VAL cc_start: 0.4219 (t) cc_final: 0.3841 (t) REVERT: L 62 PHE cc_start: 0.6137 (m-80) cc_final: 0.5816 (m-80) REVERT: L 92 PHE cc_start: 0.6219 (t80) cc_final: 0.5264 (t80) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1726 time to fit residues: 16.8490 Evaluate side-chains 74 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 10.0000 chunk 19 optimal weight: 20.0000 chunk 3 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 chunk 37 optimal weight: 0.0270 chunk 34 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 overall best weight: 2.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5675 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 3411 Z= 0.269 Angle : 0.836 10.365 4635 Z= 0.430 Chirality : 0.050 0.190 501 Planarity : 0.005 0.044 601 Dihedral : 6.832 27.566 491 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.57 % Favored : 86.43 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.73 (0.42), residues: 420 helix: -2.11 (1.17), residues: 21 sheet: -1.52 (0.42), residues: 144 loop : -2.01 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP L 35 HIS 0.001 0.001 HIS H 35 PHE 0.016 0.002 PHE A 515 TYR 0.021 0.002 TYR L 49 ARG 0.004 0.001 ARG H 101 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 408 ARG cc_start: 0.7313 (ppt170) cc_final: 0.6962 (ptm-80) REVERT: A 417 LYS cc_start: 0.7423 (ptpt) cc_final: 0.6995 (tppt) REVERT: A 424 LYS cc_start: 0.6969 (tmmt) cc_final: 0.6530 (tptp) REVERT: A 439 ASN cc_start: 0.7340 (t0) cc_final: 0.6998 (t0) REVERT: A 461 LEU cc_start: 0.6346 (mm) cc_final: 0.5969 (mm) REVERT: A 462 LYS cc_start: 0.8620 (tppt) cc_final: 0.7746 (pttm) REVERT: H 13 GLN cc_start: 0.6830 (mm-40) cc_final: 0.6047 (pm20) REVERT: H 90 ASP cc_start: 0.5636 (m-30) cc_final: 0.5405 (m-30) REVERT: H 101 ARG cc_start: 0.7531 (tpt170) cc_final: 0.6141 (ptp-170) REVERT: H 102 TYR cc_start: 0.7786 (p90) cc_final: 0.7537 (p90) REVERT: H 122 VAL cc_start: 0.4333 (t) cc_final: 0.3951 (t) REVERT: L 62 PHE cc_start: 0.5987 (m-80) cc_final: 0.5694 (m-80) REVERT: L 92 PHE cc_start: 0.6317 (t80) cc_final: 0.5625 (t80) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1553 time to fit residues: 15.3424 Evaluate side-chains 73 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.0770 chunk 33 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 0.0060 chunk 27 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 overall best weight: 2.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5656 moved from start: 0.5028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3411 Z= 0.246 Angle : 0.797 9.744 4635 Z= 0.410 Chirality : 0.048 0.165 501 Planarity : 0.005 0.042 601 Dihedral : 6.693 27.196 491 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.76 (0.42), residues: 420 helix: -2.15 (1.16), residues: 21 sheet: -1.61 (0.42), residues: 145 loop : -1.97 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP L 35 HIS 0.002 0.001 HIS H 35 PHE 0.024 0.002 PHE A 497 TYR 0.018 0.002 TYR A 453 ARG 0.004 0.001 ARG H 101 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.336 Fit side-chains REVERT: A 417 LYS cc_start: 0.7341 (ptpt) cc_final: 0.6940 (tppt) REVERT: A 424 LYS cc_start: 0.7097 (tmmt) cc_final: 0.6635 (tptp) REVERT: A 425 LEU cc_start: 0.8049 (mp) cc_final: 0.7662 (mp) REVERT: A 439 ASN cc_start: 0.7331 (t0) cc_final: 0.7006 (t0) REVERT: A 461 LEU cc_start: 0.6307 (mm) cc_final: 0.5954 (mm) REVERT: A 462 LYS cc_start: 0.8625 (tppt) cc_final: 0.7700 (ptmt) REVERT: A 515 PHE cc_start: 0.6650 (m-10) cc_final: 0.6399 (m-10) REVERT: H 13 GLN cc_start: 0.6762 (mm-40) cc_final: 0.6367 (mm-40) REVERT: H 72 ARG cc_start: 0.5588 (tpt-90) cc_final: 0.5128 (tpt-90) REVERT: H 101 ARG cc_start: 0.7486 (tpt170) cc_final: 0.7090 (mmt180) REVERT: H 102 TYR cc_start: 0.7788 (p90) cc_final: 0.7516 (p90) REVERT: L 62 PHE cc_start: 0.5972 (m-80) cc_final: 0.5671 (m-80) REVERT: L 92 PHE cc_start: 0.6599 (t80) cc_final: 0.5762 (t80) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1590 time to fit residues: 16.0470 Evaluate side-chains 75 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 20.0000 chunk 34 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 13 optimal weight: 0.0870 chunk 33 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5621 moved from start: 0.5061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3411 Z= 0.177 Angle : 0.741 8.680 4635 Z= 0.378 Chirality : 0.046 0.190 501 Planarity : 0.005 0.037 601 Dihedral : 6.033 25.529 491 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.19 % Favored : 88.81 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.59 (0.42), residues: 420 helix: -2.39 (0.99), residues: 27 sheet: -1.29 (0.44), residues: 140 loop : -1.93 (0.42), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP L 35 HIS 0.002 0.001 HIS H 35 PHE 0.013 0.001 PHE H 111 TYR 0.012 0.001 TYR A 508 ARG 0.004 0.001 ARG H 101 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: A 393 THR cc_start: 0.6509 (m) cc_final: 0.6019 (p) REVERT: A 417 LYS cc_start: 0.7308 (ptpt) cc_final: 0.6945 (tppt) REVERT: A 424 LYS cc_start: 0.7284 (tmmt) cc_final: 0.6790 (tptp) REVERT: A 425 LEU cc_start: 0.7810 (mp) cc_final: 0.7526 (mp) REVERT: A 439 ASN cc_start: 0.7441 (t0) cc_final: 0.7137 (t0) REVERT: A 461 LEU cc_start: 0.6398 (mm) cc_final: 0.6050 (mm) REVERT: A 462 LYS cc_start: 0.8634 (tppt) cc_final: 0.7714 (ptmt) REVERT: A 515 PHE cc_start: 0.6661 (m-10) cc_final: 0.6456 (m-10) REVERT: H 13 GLN cc_start: 0.6776 (mm-40) cc_final: 0.6355 (mm-40) REVERT: H 72 ARG cc_start: 0.5274 (tpt-90) cc_final: 0.4804 (ttt90) REVERT: L 92 PHE cc_start: 0.6714 (t80) cc_final: 0.5750 (t80) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1580 time to fit residues: 15.4044 Evaluate side-chains 72 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 7.9990 chunk 1 optimal weight: 0.0980 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 15 optimal weight: 0.4980 chunk 40 optimal weight: 5.9990 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 360 ASN H 39 GLN L 34 ASN L 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.170416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.145193 restraints weight = 5718.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.148820 restraints weight = 3623.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.151511 restraints weight = 2586.120| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6293 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3411 Z= 0.188 Angle : 0.751 8.714 4635 Z= 0.381 Chirality : 0.047 0.179 501 Planarity : 0.005 0.065 601 Dihedral : 6.105 26.236 491 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.61 (0.42), residues: 420 helix: -2.35 (1.00), residues: 27 sheet: -1.30 (0.43), residues: 142 loop : -1.96 (0.42), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP L 35 HIS 0.001 0.001 HIS H 35 PHE 0.009 0.001 PHE A 497 TYR 0.012 0.001 TYR L 49 ARG 0.004 0.000 ARG H 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1220.52 seconds wall clock time: 23 minutes 26.10 seconds (1406.10 seconds total)