Starting phenix.real_space_refine on Fri Apr 5 14:58:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6n_33644/04_2024/7y6n_33644.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6n_33644/04_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6n_33644/04_2024/7y6n_33644.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6n_33644/04_2024/7y6n_33644.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6n_33644/04_2024/7y6n_33644.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6n_33644/04_2024/7y6n_33644.pdb" } 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 Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 2.31, per 1000 atoms: 0.69 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 - 3.50 Amino acid : False - 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: 1.33 Conformation dependent library (CDL) restraints added in 610.9 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: 0.36 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: 0.75 Time building geometry restraints manager: 1.39 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: 100.85 - 107.46: 122 107.46 - 114.08: 1800 114.08 - 120.69: 1311 120.69 - 127.31: 1372 127.31 - 133.92: 30 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 2.520 nonbonded pdb=" OG SER L 14 " pdb=" O LYS L 107 " model vdw 2.228 2.440 nonbonded pdb=" OH TYR H 102 " pdb=" NE2 GLN L 55 " model vdw 2.266 2.520 nonbonded pdb=" O PRO L 8 " pdb=" OG1 THR L 102 " model vdw 2.269 2.440 nonbonded pdb=" OD1 ASN A 354 " pdb=" N ARG A 355 " model vdw 2.302 2.520 ... (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 ========== 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: 0.000 Extract box with map and model: 0.970 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.630 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.650 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.362 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: 0.1753 time to fit residues: 22.6718 Evaluate side-chains 77 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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: 30.0000 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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: 0.5671 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3411 Z= 0.276 Angle : 0.783 6.329 4635 Z= 0.406 Chirality : 0.048 0.178 501 Planarity : 0.006 0.065 601 Dihedral : 6.456 31.118 491 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % 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: -2.83 (0.40), residues: 420 helix: -2.24 (0.96), residues: 27 sheet: -1.65 (0.41), residues: 145 loop : -2.00 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 35 HIS 0.004 0.003 HIS H 35 PHE 0.016 0.002 PHE A 497 TYR 0.013 0.002 TYR A 505 ARG 0.005 0.001 ARG H 101 *********************** 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 86 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.6553 (mtp-110) cc_final: 0.6186 (ttm-80) REVERT: A 347 PHE cc_start: 0.7227 (m-80) cc_final: 0.6938 (m-80) REVERT: A 387 LEU cc_start: 0.5869 (tt) cc_final: 0.5497 (tp) REVERT: A 408 ARG cc_start: 0.6965 (ppt170) cc_final: 0.6736 (ptm-80) REVERT: A 417 LYS cc_start: 0.7200 (ptmt) cc_final: 0.6557 (tppt) REVERT: A 424 LYS cc_start: 0.7217 (tmmt) cc_final: 0.6830 (tptp) REVERT: A 436 TRP cc_start: 0.6656 (p90) cc_final: 0.5997 (p90) REVERT: A 439 ASN cc_start: 0.7154 (t0) cc_final: 0.6928 (t0) REVERT: A 453 TYR cc_start: 0.6679 (p90) cc_final: 0.6098 (p90) REVERT: A 461 LEU cc_start: 0.6308 (mm) cc_final: 0.6058 (mm) REVERT: H 34 MET cc_start: 0.6907 (tpt) cc_final: 0.6512 (tpt) REVERT: H 78 SER cc_start: 0.7208 (t) cc_final: 0.6550 (m) REVERT: H 101 ARG cc_start: 0.7409 (tpt170) cc_final: 0.5650 (ttm170) REVERT: H 113 PHE cc_start: 0.7418 (m-80) cc_final: 0.7211 (m-80) REVERT: L 22 THR cc_start: 0.6429 (p) cc_final: 0.6209 (m) REVERT: L 92 PHE cc_start: 0.6314 (t80) cc_final: 0.5796 (t80) REVERT: L 102 THR cc_start: 0.5452 (t) cc_final: 0.5074 (m) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1929 time to fit residues: 19.7871 Evaluate side-chains 73 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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: 1.9990 chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 37 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 33 optimal weight: 0.4980 chunk 36 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 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 L 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5610 moved from start: 0.2575 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= 0.169 Angle : 0.705 6.954 4635 Z= 0.359 Chirality : 0.047 0.191 501 Planarity : 0.004 0.033 601 Dihedral : 5.786 24.214 491 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.38 % Favored : 87.62 % 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: -2.70 (0.40), residues: 420 helix: -2.32 (0.97), residues: 27 sheet: -1.66 (0.41), residues: 144 loop : -1.82 (0.40), residues: 249 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 0.019 0.001 TYR A 365 ARG 0.005 0.000 ARG H 72 *********************** 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 81 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 408 ARG cc_start: 0.7030 (ppt170) cc_final: 0.6806 (ptm-80) REVERT: A 417 LYS cc_start: 0.7190 (ptmt) cc_final: 0.6619 (tppt) REVERT: A 424 LYS cc_start: 0.7346 (tmmt) cc_final: 0.6853 (tptp) REVERT: A 425 LEU cc_start: 0.7980 (mp) cc_final: 0.7745 (mp) REVERT: A 436 TRP cc_start: 0.6715 (p90) cc_final: 0.6039 (p90) REVERT: A 439 ASN cc_start: 0.7153 (t0) cc_final: 0.6805 (t0) REVERT: A 461 LEU cc_start: 0.6521 (mm) cc_final: 0.6311 (mm) REVERT: H 34 MET cc_start: 0.7062 (tpt) cc_final: 0.6292 (tpt) REVERT: H 78 SER cc_start: 0.7194 (t) cc_final: 0.6594 (m) REVERT: H 93 LEU cc_start: 0.6273 (mt) cc_final: 0.6028 (mt) REVERT: H 101 ARG cc_start: 0.7187 (tpt170) cc_final: 0.5720 (ttp-170) REVERT: H 113 PHE cc_start: 0.7302 (m-80) cc_final: 0.7047 (m-80) REVERT: L 92 PHE cc_start: 0.6552 (t80) cc_final: 0.5753 (t80) outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 0.1420 time to fit residues: 14.2055 Evaluate side-chains 68 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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: 9.9990 chunk 28 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN L 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5679 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 3411 Z= 0.322 Angle : 0.853 7.893 4635 Z= 0.441 Chirality : 0.051 0.240 501 Planarity : 0.005 0.032 601 Dihedral : 7.562 47.591 491 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.48 % Favored : 84.52 % Rotamer: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % 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: -2.91 (0.41), residues: 420 helix: -2.74 (0.92), residues: 27 sheet: -1.78 (0.41), residues: 143 loop : -1.94 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP L 35 HIS 0.004 0.002 HIS H 35 PHE 0.013 0.002 PHE A 486 TYR 0.024 0.003 TYR A 365 ARG 0.004 0.001 ARG H 72 *********************** 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 87 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.341 Fit side-chains REVERT: A 346 ARG cc_start: 0.6827 (mtp-110) cc_final: 0.6446 (ttm-80) REVERT: A 408 ARG cc_start: 0.7322 (ppt170) cc_final: 0.7099 (ptm-80) REVERT: A 417 LYS cc_start: 0.7261 (ptmt) cc_final: 0.6776 (tppt) REVERT: A 424 LYS cc_start: 0.7054 (tmmt) cc_final: 0.6409 (tptp) REVERT: A 439 ASN cc_start: 0.7168 (t0) cc_final: 0.6766 (t0) REVERT: A 461 LEU cc_start: 0.6363 (mm) cc_final: 0.5964 (mm) REVERT: A 462 LYS cc_start: 0.8507 (tppt) cc_final: 0.7518 (ptmt) REVERT: A 473 TYR cc_start: 0.7697 (t80) cc_final: 0.7335 (t80) REVERT: H 13 GLN cc_start: 0.6990 (mm-40) cc_final: 0.6236 (pm20) REVERT: H 78 SER cc_start: 0.7066 (t) cc_final: 0.6495 (m) REVERT: H 90 ASP cc_start: 0.4995 (m-30) cc_final: 0.4706 (m-30) REVERT: H 93 LEU cc_start: 0.6192 (mt) cc_final: 0.5888 (mt) REVERT: H 113 PHE cc_start: 0.7001 (m-80) cc_final: 0.6549 (m-80) REVERT: L 62 PHE cc_start: 0.6062 (m-80) cc_final: 0.5739 (m-80) REVERT: L 92 PHE cc_start: 0.6510 (t80) cc_final: 0.5586 (t80) REVERT: L 102 THR cc_start: 0.5264 (t) cc_final: 0.4810 (m) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1609 time to fit residues: 16.8414 Evaluate side-chains 72 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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: 9.9990 chunk 0 optimal weight: 9.9990 chunk 29 optimal weight: 0.0570 chunk 16 optimal weight: 0.1980 chunk 33 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 0.0470 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5602 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3411 Z= 0.169 Angle : 0.713 6.965 4635 Z= 0.362 Chirality : 0.046 0.195 501 Planarity : 0.004 0.034 601 Dihedral : 5.968 25.975 491 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % 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: -2.71 (0.41), residues: 420 helix: -2.76 (0.91), residues: 27 sheet: -1.66 (0.41), residues: 149 loop : -1.77 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP L 35 HIS 0.001 0.000 HIS H 35 PHE 0.017 0.002 PHE A 497 TYR 0.011 0.001 TYR A 453 ARG 0.003 0.000 ARG H 72 *********************** 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 85 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.324 Fit side-chains REVERT: A 346 ARG cc_start: 0.6789 (mtp-110) cc_final: 0.6477 (ttm-80) REVERT: A 387 LEU cc_start: 0.6432 (tp) cc_final: 0.6119 (tp) REVERT: A 408 ARG cc_start: 0.7339 (ppt170) cc_final: 0.7080 (ptm-80) REVERT: A 417 LYS cc_start: 0.6923 (ptmt) cc_final: 0.6660 (tppt) REVERT: A 424 LYS cc_start: 0.7179 (tmmt) cc_final: 0.6782 (tptp) REVERT: A 439 ASN cc_start: 0.7023 (t0) cc_final: 0.6675 (t0) REVERT: A 461 LEU cc_start: 0.6517 (mm) cc_final: 0.6253 (mm) REVERT: A 462 LYS cc_start: 0.8528 (tppt) cc_final: 0.7581 (ptmt) REVERT: H 13 GLN cc_start: 0.7051 (mm-40) cc_final: 0.6250 (pm20) REVERT: H 78 SER cc_start: 0.7142 (t) cc_final: 0.6859 (m) REVERT: H 90 ASP cc_start: 0.5110 (m-30) cc_final: 0.4873 (m-30) REVERT: H 93 LEU cc_start: 0.6085 (mt) cc_final: 0.5875 (mt) REVERT: H 113 PHE cc_start: 0.6949 (m-80) cc_final: 0.6606 (m-80) REVERT: H 122 VAL cc_start: 0.4207 (t) cc_final: 0.3887 (t) REVERT: L 39 GLU cc_start: 0.7027 (pp20) cc_final: 0.6717 (tm-30) REVERT: L 92 PHE cc_start: 0.6416 (t80) cc_final: 0.5435 (t80) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1869 time to fit residues: 18.6618 Evaluate side-chains 69 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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: 6.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 0.3980 chunk 20 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- 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: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3411 Z= 0.286 Angle : 0.805 8.187 4635 Z= 0.411 Chirality : 0.049 0.194 501 Planarity : 0.005 0.035 601 Dihedral : 6.804 36.298 491 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.05 % Favored : 85.95 % Rotamer: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % 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 (0.42), residues: 420 helix: -2.97 (0.86), residues: 27 sheet: -1.73 (0.42), residues: 143 loop : -1.77 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP L 35 HIS 0.002 0.001 HIS H 35 PHE 0.013 0.002 PHE L 98 TYR 0.014 0.002 TYR A 453 ARG 0.004 0.001 ARG H 72 *********************** 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 85 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 387 LEU cc_start: 0.6740 (tp) cc_final: 0.6401 (tp) REVERT: A 408 ARG cc_start: 0.7422 (ppt170) cc_final: 0.7064 (ptm-80) REVERT: A 417 LYS cc_start: 0.7296 (ptmt) cc_final: 0.6810 (tppt) REVERT: A 424 LYS cc_start: 0.7217 (tmmt) cc_final: 0.6599 (tptp) REVERT: A 439 ASN cc_start: 0.7039 (t0) cc_final: 0.6670 (t0) REVERT: A 461 LEU cc_start: 0.6302 (mm) cc_final: 0.5967 (mm) REVERT: A 462 LYS cc_start: 0.8495 (tppt) cc_final: 0.7526 (ptmt) REVERT: H 13 GLN cc_start: 0.6942 (mm-40) cc_final: 0.6171 (pm20) REVERT: H 78 SER cc_start: 0.7159 (t) cc_final: 0.6870 (m) REVERT: H 90 ASP cc_start: 0.5016 (m-30) cc_final: 0.4718 (m-30) REVERT: H 93 LEU cc_start: 0.6140 (mt) cc_final: 0.5928 (mt) REVERT: H 113 PHE cc_start: 0.6893 (m-80) cc_final: 0.6550 (m-80) REVERT: H 122 VAL cc_start: 0.4189 (t) cc_final: 0.3810 (t) REVERT: L 39 GLU cc_start: 0.7328 (pp20) cc_final: 0.6929 (tm-30) REVERT: L 62 PHE cc_start: 0.5946 (m-80) cc_final: 0.5637 (m-80) REVERT: L 92 PHE cc_start: 0.6584 (t80) cc_final: 0.5586 (t80) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1640 time to fit residues: 16.7836 Evaluate side-chains 76 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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: 5.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 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: 0.5661 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3411 Z= 0.256 Angle : 0.788 7.900 4635 Z= 0.406 Chirality : 0.049 0.160 501 Planarity : 0.005 0.048 601 Dihedral : 6.855 36.231 491 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.86 % Favored : 87.14 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % 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: -2.89 (0.42), residues: 420 helix: -3.00 (0.87), residues: 26 sheet: -1.88 (0.41), residues: 144 loop : -1.82 (0.43), residues: 250 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 0.020 0.002 PHE A 497 TYR 0.013 0.002 TYR A 365 ARG 0.003 0.001 ARG A 355 *********************** 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 88 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 387 LEU cc_start: 0.6644 (tp) cc_final: 0.6385 (tp) REVERT: A 417 LYS cc_start: 0.7067 (ptmt) cc_final: 0.6627 (tppt) REVERT: A 424 LYS cc_start: 0.7035 (tmmt) cc_final: 0.6504 (tptp) REVERT: A 439 ASN cc_start: 0.7079 (t0) cc_final: 0.6727 (t0) REVERT: A 461 LEU cc_start: 0.6321 (mm) cc_final: 0.5982 (mm) REVERT: A 462 LYS cc_start: 0.8512 (tppt) cc_final: 0.7568 (ptmt) REVERT: A 515 PHE cc_start: 0.7110 (m-10) cc_final: 0.6806 (m-10) REVERT: H 13 GLN cc_start: 0.6800 (mm-40) cc_final: 0.6452 (mm-40) REVERT: H 32 TYR cc_start: 0.7154 (m-10) cc_final: 0.6892 (m-10) REVERT: H 78 SER cc_start: 0.7157 (t) cc_final: 0.6868 (m) REVERT: H 90 ASP cc_start: 0.5036 (m-30) cc_final: 0.4787 (m-30) REVERT: H 113 PHE cc_start: 0.6956 (m-80) cc_final: 0.6626 (m-80) REVERT: L 39 GLU cc_start: 0.7559 (pp20) cc_final: 0.6977 (tm-30) REVERT: L 62 PHE cc_start: 0.5963 (m-80) cc_final: 0.5641 (m-80) REVERT: L 92 PHE cc_start: 0.6509 (t80) cc_final: 0.5492 (t80) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1655 time to fit residues: 17.4747 Evaluate side-chains 73 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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: 9.9990 chunk 31 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 30.0000 chunk 22 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN L 38 GLN L 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5706 moved from start: 0.5418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 3411 Z= 0.468 Angle : 1.027 8.549 4635 Z= 0.532 Chirality : 0.056 0.325 501 Planarity : 0.008 0.093 601 Dihedral : 8.423 44.440 491 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 21.93 Ramachandran Plot: Outliers : 0.24 % Allowed : 16.90 % Favored : 82.86 % 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 : 4.76 % 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: -3.43 (0.41), residues: 420 helix: -3.14 (0.99), residues: 20 sheet: -2.29 (0.41), residues: 139 loop : -2.25 (0.40), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.004 TRP L 35 HIS 0.004 0.002 HIS H 35 PHE 0.019 0.003 PHE H 68 TYR 0.036 0.004 TYR A 453 ARG 0.007 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 91 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 347 PHE cc_start: 0.7559 (m-80) cc_final: 0.7249 (m-80) REVERT: A 359 SER cc_start: 0.9052 (p) cc_final: 0.8701 (t) REVERT: A 424 LYS cc_start: 0.7057 (tmmt) cc_final: 0.6557 (tptp) REVERT: A 439 ASN cc_start: 0.7125 (t0) cc_final: 0.6796 (t0) REVERT: A 461 LEU cc_start: 0.6479 (mm) cc_final: 0.6163 (mm) REVERT: A 462 LYS cc_start: 0.8630 (tppt) cc_final: 0.7752 (ptmt) REVERT: A 473 TYR cc_start: 0.7725 (t80) cc_final: 0.7229 (t80) REVERT: H 13 GLN cc_start: 0.6664 (mm-40) cc_final: 0.6117 (pm20) REVERT: H 32 TYR cc_start: 0.7068 (m-10) cc_final: 0.6835 (m-10) REVERT: H 78 SER cc_start: 0.6880 (t) cc_final: 0.6671 (m) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1483 time to fit residues: 16.5359 Evaluate side-chains 78 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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: 8.9990 chunk 33 optimal weight: 8.9990 chunk 34 optimal weight: 0.0010 chunk 36 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 ASN L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5624 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3411 Z= 0.202 Angle : 0.797 9.690 4635 Z= 0.406 Chirality : 0.049 0.161 501 Planarity : 0.005 0.038 601 Dihedral : 7.203 42.867 491 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.19 % Favored : 88.81 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % 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: -3.25 (0.41), residues: 420 helix: -3.64 (0.75), residues: 27 sheet: -1.82 (0.42), residues: 137 loop : -2.24 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 114 HIS 0.003 0.001 HIS H 35 PHE 0.033 0.003 PHE H 68 TYR 0.024 0.002 TYR A 489 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 91 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 347 PHE cc_start: 0.7350 (m-80) cc_final: 0.6779 (m-80) REVERT: A 368 LEU cc_start: 0.6623 (mm) cc_final: 0.6296 (mt) REVERT: A 403 ARG cc_start: 0.5061 (mtm110) cc_final: 0.4705 (mtm110) REVERT: A 417 LYS cc_start: 0.7258 (ptpt) cc_final: 0.6526 (tppt) REVERT: A 424 LYS cc_start: 0.7143 (tmmt) cc_final: 0.6606 (tptt) REVERT: A 439 ASN cc_start: 0.7110 (t0) cc_final: 0.6646 (t0) REVERT: A 453 TYR cc_start: 0.6404 (p90) cc_final: 0.4468 (p90) REVERT: A 461 LEU cc_start: 0.6414 (mm) cc_final: 0.6138 (mm) REVERT: A 462 LYS cc_start: 0.8640 (tppt) cc_final: 0.7794 (ptmt) REVERT: H 13 GLN cc_start: 0.6643 (mm-40) cc_final: 0.6241 (mm-40) REVERT: H 78 SER cc_start: 0.7090 (t) cc_final: 0.6721 (m) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1642 time to fit residues: 18.1731 Evaluate side-chains 75 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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: 8.9990 chunk 3 optimal weight: 3.9990 chunk 25 optimal weight: 0.1980 chunk 19 optimal weight: 20.0000 chunk 34 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 chunk 6 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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: 0.5604 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3411 Z= 0.194 Angle : 0.781 9.215 4635 Z= 0.397 Chirality : 0.048 0.158 501 Planarity : 0.005 0.055 601 Dihedral : 6.709 28.129 491 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.86 % Favored : 87.14 % 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: -3.07 (0.41), residues: 420 helix: -3.06 (0.95), residues: 20 sheet: -1.84 (0.41), residues: 141 loop : -2.13 (0.41), residues: 259 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 0.021 0.002 PHE H 68 TYR 0.014 0.001 TYR A 453 ARG 0.006 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 89 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 393 THR cc_start: 0.6465 (m) cc_final: 0.5930 (p) REVERT: A 417 LYS cc_start: 0.7249 (ptpt) cc_final: 0.6600 (tppt) REVERT: A 424 LYS cc_start: 0.7058 (tmmt) cc_final: 0.6685 (tptt) REVERT: A 439 ASN cc_start: 0.7022 (t0) cc_final: 0.6562 (t0) REVERT: A 461 LEU cc_start: 0.6418 (mm) cc_final: 0.6122 (mm) REVERT: A 462 LYS cc_start: 0.8626 (tppt) cc_final: 0.7742 (ptmt) REVERT: H 13 GLN cc_start: 0.6673 (mm-40) cc_final: 0.6275 (mm-40) REVERT: H 78 SER cc_start: 0.7195 (t) cc_final: 0.6840 (m) REVERT: L 39 GLU cc_start: 0.7416 (tm-30) cc_final: 0.7107 (pp20) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1585 time to fit residues: 17.5454 Evaluate side-chains 75 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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: 5.9990 chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 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 360 ASN L 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.167520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.143219 restraints weight = 5746.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.146717 restraints weight = 3759.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.148848 restraints weight = 2735.992| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 moved from start: 0.5337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3411 Z= 0.183 Angle : 0.777 9.289 4635 Z= 0.390 Chirality : 0.047 0.158 501 Planarity : 0.005 0.037 601 Dihedral : 6.387 27.471 491 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.10 % Favored : 86.90 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % 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: -2.97 (0.41), residues: 420 helix: -3.15 (0.90), residues: 21 sheet: -1.73 (0.42), residues: 140 loop : -2.06 (0.41), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 35 HIS 0.002 0.001 HIS H 35 PHE 0.016 0.002 PHE H 68 TYR 0.012 0.001 TYR A 453 ARG 0.007 0.001 ARG H 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1211.37 seconds wall clock time: 22 minutes 43.55 seconds (1363.55 seconds total)