Starting phenix.real_space_refine on Mon Sep 23 13:50:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vyg_43660/09_2024/8vyg_43660.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vyg_43660/09_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_43660/09_2024/8vyg_43660.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vyg_43660/09_2024/8vyg_43660.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vyg_43660/09_2024/8vyg_43660.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vyg_43660/09_2024/8vyg_43660.cif" } 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. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 4.74, per 1000 atoms: 1.48 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG R1301 " - " ASN R 343 " Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 381.7 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: 0.45 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: 0.85 Time building geometry restraints manager: 0.85 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: 0.00 - 1.46: 3737 1.46 - 2.92: 589 2.92 - 4.38: 83 4.38 - 5.84: 33 5.84 - 7.30: 20 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 3.120 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 Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 7.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.570 Find NCS groups from input model: 0.020 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.090 ------------------------------------------------------------------------------- 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 : 0.370 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 104 average time/residue: 0.2012 time to fit residues: 24.3362 Evaluate side-chains 54 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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: 0.8980 chunk 30 optimal weight: 0.5980 chunk 16 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 11 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 A 116 ASN B 6 GLN B 90 GLN B 92 HIS R 394 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3281 Z= 0.215 Angle : 0.554 3.761 4462 Z= 0.303 Chirality : 0.045 0.141 487 Planarity : 0.005 0.027 577 Dihedral : 4.320 24.844 480 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.99 % Allowed : 10.75 % Favored : 86.27 % 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: 0.81 (0.42), residues: 408 helix: -4.00 (0.68), residues: 27 sheet: 1.46 (0.43), residues: 154 loop : 0.58 (0.40), residues: 227 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 0.011 0.001 PHE R 377 TYR 0.016 0.002 TYR B 87 ARG 0.004 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 73 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.365 Fit side-chains REVERT: A 23 LYS cc_start: 0.7508 (OUTLIER) cc_final: 0.7104 (tppt) outliers start: 10 outliers final: 5 residues processed: 69 average time/residue: 0.1958 time to fit residues: 15.8302 Evaluate side-chains 53 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 75 SER 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: 0.0970 chunk 24 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 18 optimal weight: 8.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 91 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: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3281 Z= 0.210 Angle : 0.543 5.635 4462 Z= 0.292 Chirality : 0.044 0.138 487 Planarity : 0.005 0.040 577 Dihedral : 4.420 26.092 480 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.58 % Allowed : 13.43 % Favored : 82.99 % 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: 0.52 (0.42), residues: 408 helix: -3.91 (0.72), residues: 26 sheet: 1.19 (0.41), residues: 164 loop : 0.33 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 47 HIS 0.000 0.000 HIS B 92 PHE 0.012 0.001 PHE R 377 TYR 0.018 0.002 TYR A 60 ARG 0.004 0.001 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 73 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 0.329 Fit side-chains REVERT: A 23 LYS cc_start: 0.7684 (ttmm) cc_final: 0.7392 (tppt) outliers start: 12 outliers final: 9 residues processed: 65 average time/residue: 0.1947 time to fit residues: 14.8374 Evaluate side-chains 55 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 46 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL 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 81 MET Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain R residue 389 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.5098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3281 Z= 0.331 Angle : 0.646 6.562 4462 Z= 0.337 Chirality : 0.047 0.139 487 Planarity : 0.006 0.039 577 Dihedral : 5.190 28.462 480 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.58 % Allowed : 13.43 % Favored : 82.99 % 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: 0.24 (0.42), residues: 408 helix: -3.93 (0.70), residues: 26 sheet: 1.10 (0.42), residues: 156 loop : 0.07 (0.42), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 436 HIS 0.001 0.001 HIS B 92 PHE 0.020 0.002 PHE R 377 TYR 0.015 0.002 TYR R 369 ARG 0.005 0.001 ARG R 346 *********************** 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 69 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 0.347 Fit side-chains REVERT: A 23 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7454 (tppt) outliers start: 12 outliers final: 10 residues processed: 59 average time/residue: 0.1836 time to fit residues: 12.8632 Evaluate side-chains 56 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 45 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 80 TYR Chi-restraints excluded: chain A residue 81 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.5596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3281 Z= 0.342 Angle : 0.655 7.644 4462 Z= 0.340 Chirality : 0.047 0.143 487 Planarity : 0.006 0.036 577 Dihedral : 5.381 30.531 480 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.48 % Allowed : 14.63 % 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: -0.22 (0.41), residues: 408 helix: -3.98 (0.69), residues: 26 sheet: 0.72 (0.41), residues: 166 loop : -0.27 (0.41), residues: 216 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 0.021 0.002 PHE R 377 TYR 0.028 0.002 TYR A 27 ARG 0.003 0.001 ARG A 38 *********************** 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 69 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 54 time to evaluate : 0.377 Fit side-chains REVERT: A 23 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7480 (tppt) outliers start: 15 outliers final: 12 residues processed: 59 average time/residue: 0.1840 time to fit residues: 12.9831 Evaluate side-chains 61 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 48 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 45 LEU Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain R residue 389 ASP Chi-restraints excluded: chain R residue 415 THR 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: 0.8980 chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.5713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3281 Z= 0.188 Angle : 0.543 6.124 4462 Z= 0.284 Chirality : 0.045 0.142 487 Planarity : 0.005 0.038 577 Dihedral : 4.756 26.466 480 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.28 % Allowed : 16.72 % Favored : 80.00 % 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: -0.11 (0.42), residues: 408 helix: -3.92 (0.69), residues: 26 sheet: 0.75 (0.41), residues: 166 loop : -0.16 (0.42), residues: 216 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 0.013 0.001 PHE B 72 TYR 0.015 0.002 TYR A 54 ARG 0.003 0.000 ARG A 38 *********************** 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 66 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 55 time to evaluate : 0.277 Fit side-chains REVERT: A 23 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7492 (tppt) outliers start: 11 outliers final: 8 residues processed: 57 average time/residue: 0.1977 time to fit residues: 13.2912 Evaluate side-chains 58 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 45 LEU Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain R residue 415 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.0980 chunk 32 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.0870 chunk 26 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.5801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3281 Z= 0.146 Angle : 0.507 6.156 4462 Z= 0.267 Chirality : 0.044 0.198 487 Planarity : 0.004 0.039 577 Dihedral : 4.410 25.503 480 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.99 % Allowed : 17.31 % 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: -0.02 (0.42), residues: 408 helix: -3.84 (0.69), residues: 26 sheet: 0.80 (0.40), residues: 169 loop : -0.09 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 436 HIS 0.003 0.002 HIS B 92 PHE 0.011 0.001 PHE B 72 TYR 0.020 0.001 TYR A 54 ARG 0.001 0.000 ARG R 346 *********************** 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 60 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 50 time to evaluate : 0.325 Fit side-chains REVERT: A 23 LYS cc_start: 0.7751 (ttmm) cc_final: 0.7449 (tppt) REVERT: R 369 TYR cc_start: 0.5627 (t80) cc_final: 0.5216 (t80) outliers start: 10 outliers final: 6 residues processed: 53 average time/residue: 0.1889 time to fit residues: 11.8427 Evaluate side-chains 52 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL 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 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: 6.9990 chunk 30 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.5964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3281 Z= 0.208 Angle : 0.558 7.124 4462 Z= 0.290 Chirality : 0.045 0.159 487 Planarity : 0.005 0.039 577 Dihedral : 4.662 27.486 480 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.69 % Allowed : 17.91 % Favored : 79.40 % 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: -0.04 (0.42), residues: 408 helix: -3.89 (0.68), residues: 26 sheet: 0.91 (0.40), residues: 166 loop : -0.21 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 36 HIS 0.001 0.000 HIS B 92 PHE 0.015 0.001 PHE B 72 TYR 0.020 0.002 TYR A 54 ARG 0.004 0.000 ARG A 38 *********************** 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 61 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 52 time to evaluate : 0.357 Fit side-chains REVERT: A 23 LYS cc_start: 0.7751 (ttmm) cc_final: 0.7477 (tppt) REVERT: R 369 TYR cc_start: 0.5630 (t80) cc_final: 0.5273 (t80) outliers start: 9 outliers final: 9 residues processed: 56 average time/residue: 0.1646 time to fit residues: 11.2094 Evaluate side-chains 55 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 46 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 75 SER Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 91 GLN 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: 5.9990 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 26 optimal weight: 0.0070 chunk 39 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 31 optimal weight: 0.0870 chunk 3 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.6021 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= 0.146 Angle : 0.525 7.607 4462 Z= 0.269 Chirality : 0.044 0.137 487 Planarity : 0.004 0.038 577 Dihedral : 4.256 24.547 480 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % 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: 0.13 (0.42), residues: 408 helix: -3.74 (0.70), residues: 26 sheet: 0.95 (0.40), residues: 169 loop : -0.04 (0.44), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 36 HIS 0.003 0.002 HIS B 92 PHE 0.009 0.001 PHE B 72 TYR 0.017 0.001 TYR A 54 ARG 0.003 0.000 ARG A 38 *********************** 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 59 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 50 time to evaluate : 0.371 Fit side-chains REVERT: A 23 LYS cc_start: 0.7763 (ttmm) cc_final: 0.7459 (tppt) REVERT: R 369 TYR cc_start: 0.5605 (t80) cc_final: 0.5141 (t80) outliers start: 9 outliers final: 7 residues processed: 54 average time/residue: 0.1728 time to fit residues: 11.3771 Evaluate side-chains 51 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 75 SER 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 B residue 91 GLN Chi-restraints excluded: chain R residue 389 ASP 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: 3.9990 chunk 29 optimal weight: 0.0040 chunk 4 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 overall best weight: 1.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.6145 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= 0.265 Angle : 0.611 7.715 4462 Z= 0.314 Chirality : 0.047 0.143 487 Planarity : 0.005 0.039 577 Dihedral : 4.817 28.313 480 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.99 % Allowed : 19.10 % Favored : 77.91 % 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: 0.01 (0.42), residues: 408 helix: -3.82 (0.72), residues: 26 sheet: 1.00 (0.40), residues: 166 loop : -0.23 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 47 HIS 0.003 0.002 HIS B 92 PHE 0.017 0.002 PHE B 72 TYR 0.018 0.002 TYR A 54 ARG 0.002 0.000 ARG A 38 ********************** 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 55 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 45 time to evaluate : 0.356 Fit side-chains REVERT: A 23 LYS cc_start: 0.7752 (ttmm) cc_final: 0.7479 (tppt) REVERT: R 369 TYR cc_start: 0.5689 (t80) cc_final: 0.5350 (t80) outliers start: 10 outliers final: 9 residues processed: 50 average time/residue: 0.1727 time to fit residues: 10.5407 Evaluate side-chains 51 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 75 SER 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 B residue 91 GLN Chi-restraints excluded: chain R residue 389 ASP Chi-restraints excluded: chain R residue 393 THR 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: 1.9990 chunk 36 optimal weight: 0.6980 chunk 21 optimal weight: 0.0570 chunk 27 optimal weight: 0.2980 chunk 1 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.170161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.139463 restraints weight = 5838.158| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.44 r_work: 0.3727 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.6147 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= 0.157 Angle : 0.548 10.240 4462 Z= 0.278 Chirality : 0.044 0.138 487 Planarity : 0.004 0.038 577 Dihedral : 4.343 24.352 480 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.09 % Allowed : 20.30 % Favored : 77.61 % 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: 0.09 (0.42), residues: 408 helix: -3.67 (0.74), residues: 26 sheet: 0.96 (0.40), residues: 166 loop : -0.10 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 47 HIS 0.002 0.002 HIS B 92 PHE 0.015 0.001 PHE R 497 TYR 0.017 0.001 TYR A 54 ARG 0.002 0.000 ARG A 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1464.86 seconds wall clock time: 26 minutes 43.72 seconds (1603.72 seconds total)