Starting phenix.real_space_refine on Fri Apr 5 14:15:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vyg_43660/04_2024/8vyg_43660.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vyg_43660/04_2024/8vyg_43660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vyg_43660/04_2024/8vyg_43660.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vyg_43660/04_2024/8vyg_43660.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vyg_43660/04_2024/8vyg_43660.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vyg_43660/04_2024/8vyg_43660.pdb" } resolution = 3.1 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= 0.054 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 13 5.16 5 C 2028 2.51 5 N 545 2.21 5 O 618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "A TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 99": "OD1" <-> "OD2" Residue "B PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 515": "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: 3204 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 975 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 122} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 795 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "R" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1420 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 10, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "R" 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: 2.21, per 1000 atoms: 0.69 Number of scatterers: 3204 At special positions: 0 Unit cell: (92.73, 64.068, 80.085, 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 13 16.00 O 618 8.00 N 545 7.00 C 2028 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 89 " distance=2.05 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.05 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.05 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 R1301 " - " ASN R 343 " Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 631.2 milliseconds 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 752 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 8 sheets defined 13.9% alpha, 32.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.540A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.941A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'R' and resid 338 through 343 Processing helix chain 'R' and resid 349 through 353 Processing helix chain 'R' and resid 365 through 370 Processing helix chain 'R' and resid 386 through 389 Processing helix chain 'R' and resid 405 through 410 removed outlier: 4.609A pdb=" N ARG R 408 " --> pdb=" O ASP R 405 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'R' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.778A pdb=" N GLY A 33 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 12 removed outlier: 7.260A pdb=" N LEU B 34 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N TYR B 50 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TRP B 36 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 Processing sheet with id=AA6, first strand: chain 'R' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'R' and resid 361 through 362 removed outlier: 6.567A pdb=" N CYS R 361 " --> pdb=" O CYS R 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 452 through 454 120 hydrogen bonds defined for protein. 276 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: 0.88 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 606 1.32 - 1.45: 904 1.45 - 1.58: 1754 1.58 - 1.71: 1 1.71 - 1.84: 16 Bond restraints: 3281 Sorted by residual: bond pdb=" N LEU R 517 " pdb=" CA LEU R 517 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.20e-02 6.94e+03 8.65e+00 bond pdb=" N ARG R 346 " pdb=" CA ARG R 346 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.24e-02 6.50e+03 8.58e+00 bond pdb=" N ILE B 49 " pdb=" CA ILE B 49 " ideal model delta sigma weight residual 1.458 1.493 -0.034 1.17e-02 7.31e+03 8.55e+00 bond pdb=" N LYS R 378 " pdb=" CA LYS R 378 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.21e-02 6.83e+03 8.19e+00 bond pdb=" N TYR R 449 " pdb=" CA TYR R 449 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.18e-02 7.18e+03 7.92e+00 ... (remaining 3276 not shown) Histogram of bond angle deviations from ideal: 100.32 - 107.03: 103 107.03 - 113.74: 1709 113.74 - 120.45: 1269 120.45 - 127.16: 1359 127.16 - 133.87: 22 Bond angle restraints: 4462 Sorted by residual: angle pdb=" C CYS R 383 " pdb=" N PRO R 384 " pdb=" CA PRO R 384 " ideal model delta sigma weight residual 119.56 126.86 -7.30 1.02e+00 9.61e-01 5.12e+01 angle pdb=" C GLN R 498 " pdb=" N PRO R 499 " pdb=" CA PRO R 499 " ideal model delta sigma weight residual 119.56 126.70 -7.14 1.01e+00 9.80e-01 4.99e+01 angle pdb=" C ILE B 59 " pdb=" N PRO B 60 " pdb=" CA PRO B 60 " ideal model delta sigma weight residual 119.78 126.92 -7.14 1.03e+00 9.43e-01 4.81e+01 angle pdb=" C SER R 490 " pdb=" N PRO R 491 " pdb=" CA PRO R 491 " ideal model delta sigma weight residual 119.19 126.46 -7.27 1.06e+00 8.90e-01 4.71e+01 angle pdb=" C ALA R 411 " pdb=" N PRO R 412 " pdb=" CA PRO R 412 " ideal model delta sigma weight residual 119.76 126.78 -7.02 1.03e+00 9.43e-01 4.65e+01 ... (remaining 4457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.97: 1815 13.97 - 27.93: 75 27.93 - 41.90: 28 41.90 - 55.86: 7 55.86 - 69.83: 8 Dihedral angle restraints: 1933 sinusoidal: 744 harmonic: 1189 Sorted by residual: dihedral pdb=" CB CYS B 23 " pdb=" SG CYS B 23 " pdb=" SG CYS B 89 " pdb=" CB CYS B 89 " ideal model delta sinusoidal sigma weight residual 93.00 58.37 34.63 1 1.00e+01 1.00e-02 1.70e+01 dihedral pdb=" C ASP R 427 " pdb=" N ASP R 427 " pdb=" CA ASP R 427 " pdb=" CB ASP R 427 " ideal model delta harmonic sigma weight residual -122.60 -131.83 9.23 0 2.50e+00 1.60e-01 1.36e+01 dihedral pdb=" C PHE R 377 " pdb=" N PHE R 377 " pdb=" CA PHE R 377 " pdb=" CB PHE R 377 " ideal model delta harmonic sigma weight residual -122.60 -113.75 -8.85 0 2.50e+00 1.60e-01 1.25e+01 ... (remaining 1930 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 353 0.069 - 0.138: 103 0.138 - 0.207: 24 0.207 - 0.276: 4 0.276 - 0.345: 3 Chirality restraints: 487 Sorted by residual: chirality pdb=" C2 NAG R1301 " pdb=" C1 NAG R1301 " pdb=" C3 NAG R1301 " pdb=" N2 NAG R1301 " both_signs ideal model delta sigma weight residual False -2.49 -2.84 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CA TYR R 495 " pdb=" N TYR R 495 " pdb=" C TYR R 495 " pdb=" CB TYR R 495 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA ASP R 427 " pdb=" N ASP R 427 " pdb=" C ASP R 427 " pdb=" CB ASP R 427 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 484 not shown) Planarity restraints: 578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 36 " 0.023 2.00e-02 2.50e+03 1.19e-02 3.55e+00 pdb=" CG TRP B 36 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP B 36 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP B 36 " -0.016 2.00e-02 2.50e+03 pdb=" NE1 TRP B 36 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 36 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP B 36 " -0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 36 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 36 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 36 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 377 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.27e+00 pdb=" C PHE R 377 " 0.031 2.00e-02 2.50e+03 pdb=" O PHE R 377 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS R 378 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 50 " -0.024 2.00e-02 2.50e+03 1.14e-02 3.22e+00 pdb=" CG TRP A 50 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TRP A 50 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 50 " 0.014 2.00e-02 2.50e+03 pdb=" NE1 TRP A 50 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 50 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 50 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 50 " -0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 50 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 50 " -0.012 2.00e-02 2.50e+03 ... (remaining 575 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 1656 2.99 - 3.47: 2694 3.47 - 3.95: 5343 3.95 - 4.42: 6021 4.42 - 4.90: 9767 Nonbonded interactions: 25481 Sorted by model distance: nonbonded pdb=" O ASP R 427 " pdb=" OD1 ASP R 427 " model vdw 2.515 3.040 nonbonded pdb=" N ASP R 428 " pdb=" OD1 ASP R 428 " model vdw 2.532 2.520 nonbonded pdb=" O PHE R 377 " pdb=" CB PHE R 377 " model vdw 2.608 2.752 nonbonded pdb=" N GLU B 80 " pdb=" O GLU B 80 " model vdw 2.612 2.496 nonbonded pdb=" N GLY R 416 " pdb=" O GLY R 416 " model vdw 2.615 2.496 ... (remaining 25476 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.710 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: 27.770 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.530 Find NCS groups from input model: 0.090 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 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 : 0.010 0.054 3281 Z= 0.673 Angle : 1.217 7.296 4462 Z= 0.839 Chirality : 0.073 0.345 487 Planarity : 0.005 0.018 577 Dihedral : 10.292 69.829 1166 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 0.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.30 % Allowed : 0.60 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.41), residues: 408 helix: -4.23 (0.43), residues: 31 sheet: 1.32 (0.42), residues: 144 loop : 0.69 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.006 TRP A 50 HIS 0.002 0.001 HIS B 92 PHE 0.014 0.003 PHE R 497 TYR 0.017 0.003 TYR A 95 ARG 0.002 0.000 ARG R 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 0.368 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 104 average time/residue: 0.2057 time to fit residues: 24.7448 Evaluate side-chains 54 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 116 ASN B 6 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3281 Z= 0.220 Angle : 0.558 4.082 4462 Z= 0.303 Chirality : 0.045 0.140 487 Planarity : 0.005 0.029 577 Dihedral : 4.403 24.344 480 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.28 % Allowed : 11.04 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.42), residues: 408 helix: -4.16 (0.83), residues: 20 sheet: 1.40 (0.43), residues: 154 loop : 0.45 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 47 HIS 0.001 0.001 HIS B 92 PHE 0.010 0.001 PHE R 377 TYR 0.016 0.002 TYR B 87 ARG 0.003 0.001 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 time to evaluate : 0.378 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 61 average time/residue: 0.2109 time to fit residues: 15.3648 Evaluate side-chains 55 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain R residue 389 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 18 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN B 6 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3281 Z= 0.189 Angle : 0.507 5.374 4462 Z= 0.271 Chirality : 0.043 0.138 487 Planarity : 0.005 0.041 577 Dihedral : 4.207 24.782 480 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.58 % Allowed : 11.94 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.41), residues: 408 helix: -3.81 (0.72), residues: 26 sheet: 1.17 (0.41), residues: 164 loop : 0.30 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 47 HIS 0.001 0.000 HIS B 92 PHE 0.011 0.001 PHE R 377 TYR 0.015 0.002 TYR A 60 ARG 0.003 0.000 ARG R 346 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 56 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 23 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.7457 (tppt) REVERT: R 356 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7595 (ttmm) outliers start: 12 outliers final: 6 residues processed: 61 average time/residue: 0.2143 time to fit residues: 15.3824 Evaluate side-chains 54 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain R residue 356 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 21 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN B 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3281 Z= 0.175 Angle : 0.495 4.887 4462 Z= 0.260 Chirality : 0.044 0.139 487 Planarity : 0.005 0.039 577 Dihedral : 4.244 24.964 480 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.69 % Allowed : 13.43 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.42), residues: 408 helix: -3.71 (0.74), residues: 26 sheet: 1.17 (0.41), residues: 164 loop : 0.36 (0.43), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 47 HIS 0.001 0.001 HIS B 92 PHE 0.011 0.001 PHE R 377 TYR 0.016 0.001 TYR R 380 ARG 0.002 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 50 time to evaluate : 0.363 Fit side-chains REVERT: A 23 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7519 (tppt) outliers start: 9 outliers final: 7 residues processed: 54 average time/residue: 0.2206 time to fit residues: 13.8891 Evaluate side-chains 52 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain R residue 389 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 0.0980 chunk 22 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN B 38 GLN B 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 3281 Z= 0.183 Angle : 0.494 5.053 4462 Z= 0.260 Chirality : 0.044 0.138 487 Planarity : 0.005 0.039 577 Dihedral : 4.276 25.523 480 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.28 % Allowed : 14.33 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.42), residues: 408 helix: -3.69 (0.74), residues: 26 sheet: 1.00 (0.40), residues: 168 loop : 0.36 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 47 HIS 0.001 0.001 HIS B 92 PHE 0.011 0.001 PHE R 377 TYR 0.015 0.001 TYR R 380 ARG 0.002 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 54 time to evaluate : 0.409 Fit side-chains REVERT: A 23 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7517 (tppt) REVERT: A 48 MET cc_start: 0.7143 (OUTLIER) cc_final: 0.6647 (ttp) REVERT: A 65 GLN cc_start: 0.5782 (mt0) cc_final: 0.5478 (tt0) REVERT: R 369 TYR cc_start: 0.5675 (t80) cc_final: 0.5314 (t80) outliers start: 11 outliers final: 7 residues processed: 58 average time/residue: 0.2129 time to fit residues: 14.5341 Evaluate side-chains 54 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain R residue 389 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 28 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.5254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3281 Z= 0.182 Angle : 0.495 5.301 4462 Z= 0.258 Chirality : 0.044 0.139 487 Planarity : 0.005 0.039 577 Dihedral : 4.264 25.371 480 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.58 % Allowed : 14.93 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.43), residues: 408 helix: -3.67 (0.76), residues: 26 sheet: 1.08 (0.41), residues: 165 loop : 0.28 (0.43), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 47 HIS 0.001 0.001 HIS B 92 PHE 0.012 0.001 PHE B 72 TYR 0.020 0.002 TYR A 54 ARG 0.002 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 53 time to evaluate : 0.349 Fit side-chains REVERT: A 23 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7530 (tppt) REVERT: A 48 MET cc_start: 0.7203 (OUTLIER) cc_final: 0.6729 (ttp) REVERT: A 65 GLN cc_start: 0.5845 (mt0) cc_final: 0.5598 (tt0) REVERT: R 356 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7548 (ttmm) REVERT: R 369 TYR cc_start: 0.5667 (t80) cc_final: 0.5302 (t80) outliers start: 12 outliers final: 9 residues processed: 59 average time/residue: 0.2231 time to fit residues: 15.2824 Evaluate side-chains 63 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 51 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain R residue 356 LYS Chi-restraints excluded: chain R residue 389 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.0670 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.5349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3281 Z= 0.161 Angle : 0.486 5.229 4462 Z= 0.252 Chirality : 0.044 0.140 487 Planarity : 0.004 0.039 577 Dihedral : 4.171 24.978 480 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.88 % Allowed : 14.33 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.43), residues: 408 helix: -3.63 (0.76), residues: 26 sheet: 1.02 (0.41), residues: 168 loop : 0.27 (0.43), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 47 HIS 0.001 0.001 HIS B 92 PHE 0.013 0.001 PHE B 72 TYR 0.017 0.001 TYR A 54 ARG 0.001 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 51 time to evaluate : 0.369 Fit side-chains REVERT: A 23 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7538 (tppt) REVERT: A 48 MET cc_start: 0.7116 (OUTLIER) cc_final: 0.6721 (ttm) REVERT: R 356 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7492 (ttmm) REVERT: R 369 TYR cc_start: 0.5632 (t80) cc_final: 0.5264 (t80) outliers start: 13 outliers final: 9 residues processed: 57 average time/residue: 0.2205 time to fit residues: 14.6327 Evaluate side-chains 61 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 49 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain R residue 356 LYS Chi-restraints excluded: chain R residue 389 ASP Chi-restraints excluded: chain R residue 415 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 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 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.5651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3281 Z= 0.268 Angle : 0.570 6.430 4462 Z= 0.293 Chirality : 0.046 0.141 487 Planarity : 0.005 0.040 577 Dihedral : 4.743 28.120 480 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.88 % Allowed : 15.22 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.42), residues: 408 helix: -3.71 (0.76), residues: 26 sheet: 1.02 (0.41), residues: 165 loop : 0.09 (0.43), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 47 HIS 0.001 0.001 HIS B 92 PHE 0.017 0.002 PHE B 72 TYR 0.017 0.002 TYR A 54 ARG 0.002 0.000 ARG R 457 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 57 time to evaluate : 0.351 Fit side-chains REVERT: A 23 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7565 (tppt) REVERT: R 356 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7589 (ttmm) REVERT: R 369 TYR cc_start: 0.5741 (t80) cc_final: 0.5404 (t80) outliers start: 13 outliers final: 9 residues processed: 63 average time/residue: 0.2096 time to fit residues: 15.5482 Evaluate side-chains 62 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 51 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain R residue 356 LYS Chi-restraints excluded: chain R residue 389 ASP Chi-restraints excluded: chain R residue 415 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 26 optimal weight: 0.0670 chunk 39 optimal weight: 0.0470 chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 65 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.5677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3281 Z= 0.142 Angle : 0.511 6.213 4462 Z= 0.266 Chirality : 0.044 0.142 487 Planarity : 0.005 0.042 577 Dihedral : 4.185 23.416 480 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.69 % Allowed : 17.61 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.42), residues: 408 helix: -3.60 (0.76), residues: 26 sheet: 1.00 (0.40), residues: 168 loop : 0.20 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 47 HIS 0.000 0.000 HIS B 92 PHE 0.009 0.001 PHE B 72 TYR 0.033 0.002 TYR A 27 ARG 0.002 0.000 ARG R 355 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 52 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.6947 (OUTLIER) cc_final: 0.6656 (ttm) REVERT: R 369 TYR cc_start: 0.5591 (t80) cc_final: 0.5180 (t80) outliers start: 9 outliers final: 8 residues processed: 56 average time/residue: 0.1850 time to fit residues: 12.4703 Evaluate side-chains 58 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain R residue 389 ASP Chi-restraints excluded: chain R residue 415 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 0.0980 chunk 1 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.5857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3281 Z= 0.212 Angle : 0.563 9.177 4462 Z= 0.284 Chirality : 0.045 0.139 487 Planarity : 0.005 0.043 577 Dihedral : 4.522 26.048 480 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.69 % Allowed : 18.21 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.42), residues: 408 helix: -3.60 (0.79), residues: 26 sheet: 1.01 (0.40), residues: 165 loop : 0.04 (0.43), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 47 HIS 0.001 0.001 HIS B 92 PHE 0.013 0.001 PHE B 72 TYR 0.034 0.002 TYR A 27 ARG 0.002 0.000 ARG R 355 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 51 time to evaluate : 0.371 Fit side-chains REVERT: R 369 TYR cc_start: 0.5707 (t80) cc_final: 0.5352 (t80) outliers start: 9 outliers final: 9 residues processed: 55 average time/residue: 0.1906 time to fit residues: 12.5130 Evaluate side-chains 56 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 47 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain R residue 389 ASP Chi-restraints excluded: chain R residue 415 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.5980 chunk 36 optimal weight: 0.0970 chunk 21 optimal weight: 0.0570 chunk 27 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 14 optimal weight: 0.5980 chunk 39 optimal weight: 0.3980 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.170907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.139726 restraints weight = 5840.305| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.47 r_work: 0.3728 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.5880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3281 Z= 0.133 Angle : 0.527 9.205 4462 Z= 0.264 Chirality : 0.043 0.139 487 Planarity : 0.004 0.043 577 Dihedral : 4.107 22.875 480 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.39 % Allowed : 18.51 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.42), residues: 408 helix: -3.55 (0.76), residues: 26 sheet: 0.95 (0.40), residues: 168 loop : 0.18 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 47 HIS 0.001 0.001 HIS B 92 PHE 0.008 0.001 PHE B 72 TYR 0.030 0.002 TYR A 27 ARG 0.001 0.000 ARG R 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1558.16 seconds wall clock time: 28 minutes 50.29 seconds (1730.29 seconds total)