Starting phenix.real_space_refine on Thu Jul 18 19:25:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tma_41382/07_2024/8tma_41382.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tma_41382/07_2024/8tma_41382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tma_41382/07_2024/8tma_41382.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tma_41382/07_2024/8tma_41382.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tma_41382/07_2024/8tma_41382.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tma_41382/07_2024/8tma_41382.cif" } resolution = 3.2 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= -0.009 sd= 0.098 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 11 5.16 5 C 2083 2.51 5 N 539 2.21 5 O 621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 3254 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1407 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1015 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 120} Chain: "L" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 832 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 3.67, per 1000 atoms: 1.13 Number of scatterers: 3254 At special positions: 0 Unit cell: (72.6, 86.9, 79.2, 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 11 16.00 O 621 8.00 N 539 7.00 C 2083 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 675.9 milliseconds 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 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: 8 helices and 8 sheets defined 11.2% alpha, 38.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.570A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.490A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.415A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.754A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 357 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.606A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.614A pdb=" N VAL H 109 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.814A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASN H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.813A pdb=" N TRP H 35A" --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N TYR H 52 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N TYR H 34 " --> pdb=" O TYR H 52 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR H 35 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER H 35B" --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.628A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.185A pdb=" N GLN L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 10.044A pdb=" N SER L 67 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 12.317A pdb=" N ILE L 29 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 12.302A pdb=" N SER L 65 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.512A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.512A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 104 hydrogen bonds defined for protein. 252 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.75 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1026 1.34 - 1.46: 933 1.46 - 1.58: 1376 1.58 - 1.70: 0 1.70 - 1.82: 13 Bond restraints: 3348 Sorted by residual: bond pdb=" CG1 ILE A 434 " pdb=" CD1 ILE A 434 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.52e-01 bond pdb=" CB PRO A 337 " pdb=" CG PRO A 337 " ideal model delta sigma weight residual 1.492 1.535 -0.043 5.00e-02 4.00e+02 7.49e-01 bond pdb=" N ASN H 65 " pdb=" CA ASN H 65 " ideal model delta sigma weight residual 1.460 1.473 -0.013 1.54e-02 4.22e+03 7.00e-01 bond pdb=" CG LEU H 20 " pdb=" CD1 LEU H 20 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.93e-01 bond pdb=" SD MET L 4 " pdb=" CE MET L 4 " ideal model delta sigma weight residual 1.791 1.773 0.018 2.50e-02 1.60e+03 5.39e-01 ... (remaining 3343 not shown) Histogram of bond angle deviations from ideal: 100.58 - 107.26: 117 107.26 - 113.94: 1728 113.94 - 120.62: 1297 120.62 - 127.30: 1374 127.30 - 133.98: 41 Bond angle restraints: 4557 Sorted by residual: angle pdb=" CB MET L 4 " pdb=" CG MET L 4 " pdb=" SD MET L 4 " ideal model delta sigma weight residual 112.70 105.31 7.39 3.00e+00 1.11e-01 6.06e+00 angle pdb=" C ASN H 64 " pdb=" N ASN H 65 " pdb=" CA ASN H 65 " ideal model delta sigma weight residual 122.46 125.80 -3.34 1.41e+00 5.03e-01 5.60e+00 angle pdb=" C ASP L 50 " pdb=" N ALA L 51 " pdb=" CA ALA L 51 " ideal model delta sigma weight residual 121.54 125.89 -4.35 1.91e+00 2.74e-01 5.19e+00 angle pdb=" CA CYS H 22 " pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " ideal model delta sigma weight residual 114.40 119.03 -4.63 2.30e+00 1.89e-01 4.06e+00 angle pdb=" CA CYS L 88 " pdb=" CB CYS L 88 " pdb=" SG CYS L 88 " ideal model delta sigma weight residual 114.40 118.60 -4.20 2.30e+00 1.89e-01 3.33e+00 ... (remaining 4552 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 1784 16.87 - 33.74: 135 33.74 - 50.61: 12 50.61 - 67.48: 5 67.48 - 84.35: 4 Dihedral angle restraints: 1940 sinusoidal: 752 harmonic: 1188 Sorted by residual: dihedral pdb=" CA GLN L 89 " pdb=" CB GLN L 89 " pdb=" CG GLN L 89 " pdb=" CD GLN L 89 " ideal model delta sinusoidal sigma weight residual -60.00 -114.44 54.44 3 1.50e+01 4.44e-03 9.28e+00 dihedral pdb=" CG ARG H 100A" pdb=" CD ARG H 100A" pdb=" NE ARG H 100A" pdb=" CZ ARG H 100A" ideal model delta sinusoidal sigma weight residual -90.00 -128.39 38.39 2 1.50e+01 4.44e-03 8.23e+00 dihedral pdb=" CA LEU L 33 " pdb=" CB LEU L 33 " pdb=" CG LEU L 33 " pdb=" CD1 LEU L 33 " ideal model delta sinusoidal sigma weight residual 180.00 135.68 44.32 3 1.50e+01 4.44e-03 7.97e+00 ... (remaining 1937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 250 0.032 - 0.063: 160 0.063 - 0.095: 34 0.095 - 0.127: 24 0.127 - 0.158: 10 Chirality restraints: 478 Sorted by residual: chirality pdb=" CA ILE A 434 " pdb=" N ILE A 434 " pdb=" C ILE A 434 " pdb=" CB ILE A 434 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.28e-01 chirality pdb=" CA ILE H 37 " pdb=" N ILE H 37 " pdb=" C ILE H 37 " pdb=" CB ILE H 37 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.50e-01 ... (remaining 475 not shown) Planarity restraints: 587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 408 " 0.320 9.50e-02 1.11e+02 1.45e-01 1.69e+01 pdb=" NE ARG A 408 " -0.031 2.00e-02 2.50e+03 pdb=" CZ ARG A 408 " 0.032 2.00e-02 2.50e+03 pdb=" NH1 ARG A 408 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG A 408 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 466 " 0.122 9.50e-02 1.11e+02 5.51e-02 2.31e+00 pdb=" NE ARG A 466 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 466 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 466 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 466 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 100A" 0.108 9.50e-02 1.11e+02 4.89e-02 1.95e+00 pdb=" NE ARG H 100A" -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG H 100A" 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG H 100A" -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG H 100A" -0.000 2.00e-02 2.50e+03 ... (remaining 584 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1109 2.84 - 3.35: 2644 3.35 - 3.87: 4739 3.87 - 4.38: 5348 4.38 - 4.90: 10154 Nonbonded interactions: 23994 Sorted by model distance: nonbonded pdb=" NH1 ARG A 457 " pdb=" O SER A 459 " model vdw 2.324 2.520 nonbonded pdb=" OE1 GLU A 406 " pdb=" NE2 GLN A 409 " model vdw 2.328 2.520 nonbonded pdb=" OG SER L 14 " pdb=" OD2 ASP L 17 " model vdw 2.345 2.440 nonbonded pdb=" OG SER A 349 " pdb=" O LEU A 452 " model vdw 2.380 2.440 nonbonded pdb=" NH2 ARG A 357 " pdb=" OD1 ASN A 394 " model vdw 2.394 2.520 ... (remaining 23989 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.490 Find NCS groups from input model: 0.030 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3348 Z= 0.228 Angle : 0.682 7.387 4557 Z= 0.360 Chirality : 0.048 0.158 478 Planarity : 0.008 0.145 587 Dihedral : 12.057 84.349 1176 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.98 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.56 (0.39), residues: 402 helix: -4.09 (0.60), residues: 25 sheet: 0.34 (0.49), residues: 124 loop : -1.49 (0.33), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 96 HIS 0.002 0.001 HIS H 40 PHE 0.018 0.002 PHE H 29 TYR 0.020 0.003 TYR H 91 ARG 0.036 0.003 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: H 14 PRO cc_start: 0.6060 (Cg_endo) cc_final: 0.5845 (Cg_exo) REVERT: L 90 GLN cc_start: 0.8353 (pp30) cc_final: 0.7946 (pp30) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1690 time to fit residues: 18.6528 Evaluate side-chains 58 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 35 optimal weight: 0.0000 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN A 474 GLN A 501 ASN H 6 GLN L 92 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3348 Z= 0.277 Angle : 0.649 6.016 4557 Z= 0.342 Chirality : 0.048 0.157 478 Planarity : 0.005 0.032 587 Dihedral : 5.021 43.741 456 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.69 % Allowed : 7.34 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.04 (0.39), residues: 402 helix: -3.39 (0.63), residues: 31 sheet: 0.98 (0.50), residues: 120 loop : -1.24 (0.35), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 96 HIS 0.003 0.001 HIS H 40 PHE 0.017 0.002 PHE H 29 TYR 0.017 0.002 TYR H 91 ARG 0.006 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 0.370 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 59 average time/residue: 0.1796 time to fit residues: 12.6981 Evaluate side-chains 59 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 0.0270 chunk 38 optimal weight: 0.0000 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 0.0670 chunk 28 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3348 Z= 0.165 Angle : 0.531 5.422 4557 Z= 0.280 Chirality : 0.044 0.144 478 Planarity : 0.004 0.031 587 Dihedral : 4.638 45.644 456 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.41 % Allowed : 10.17 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.70 (0.41), residues: 402 helix: -3.10 (0.71), residues: 31 sheet: 0.94 (0.46), residues: 140 loop : -1.00 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.002 0.001 HIS H 40 PHE 0.011 0.001 PHE A 377 TYR 0.011 0.001 TYR H 91 ARG 0.003 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 59 average time/residue: 0.1705 time to fit residues: 12.1152 Evaluate side-chains 56 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 0.1980 chunk 16 optimal weight: 0.0030 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 0.0030 chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 21 optimal weight: 0.0030 chunk 0 optimal weight: 0.9990 overall best weight: 0.1810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3348 Z= 0.127 Angle : 0.500 5.596 4557 Z= 0.259 Chirality : 0.043 0.141 478 Planarity : 0.004 0.028 587 Dihedral : 4.236 39.904 456 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.39 % Allowed : 9.32 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.39 (0.41), residues: 402 helix: -2.97 (0.76), residues: 31 sheet: 1.15 (0.46), residues: 140 loop : -0.77 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.001 0.000 HIS H 77 PHE 0.009 0.001 PHE A 377 TYR 0.010 0.001 TYR H 59 ARG 0.005 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 0.388 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 63 average time/residue: 0.1639 time to fit residues: 12.5351 Evaluate side-chains 61 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.5980 chunk 15 optimal weight: 0.0670 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 0.0060 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 overall best weight: 0.3334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3348 Z= 0.166 Angle : 0.517 5.505 4557 Z= 0.271 Chirality : 0.043 0.143 478 Planarity : 0.004 0.028 587 Dihedral : 4.221 36.157 456 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.26 % Allowed : 11.02 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.31 (0.41), residues: 402 helix: -3.14 (0.74), residues: 31 sheet: 0.99 (0.45), residues: 150 loop : -0.59 (0.39), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.002 0.001 HIS H 101 PHE 0.010 0.001 PHE A 377 TYR 0.012 0.001 TYR H 91 ARG 0.005 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.329 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 59 average time/residue: 0.1553 time to fit residues: 11.1709 Evaluate side-chains 62 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 0.5980 chunk 37 optimal weight: 0.2980 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 0.0770 chunk 19 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 21 optimal weight: 0.3980 chunk 27 optimal weight: 0.6980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3348 Z= 0.193 Angle : 0.538 5.447 4557 Z= 0.283 Chirality : 0.044 0.138 478 Planarity : 0.004 0.026 587 Dihedral : 4.287 33.479 456 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.39 % Allowed : 10.17 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.36 (0.41), residues: 402 helix: -3.24 (0.73), residues: 31 sheet: 1.03 (0.45), residues: 150 loop : -0.67 (0.38), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS H 101 PHE 0.009 0.001 PHE H 53 TYR 0.013 0.001 TYR H 91 ARG 0.005 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 54 time to evaluate : 0.381 Fit side-chains REVERT: L 55 GLU cc_start: 0.8037 (tp30) cc_final: 0.7824 (tp30) outliers start: 12 outliers final: 9 residues processed: 61 average time/residue: 0.1587 time to fit residues: 11.8544 Evaluate side-chains 62 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 0.0770 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 11 optimal weight: 0.1980 chunk 7 optimal weight: 0.6980 chunk 25 optimal weight: 0.0030 chunk 18 optimal weight: 0.1980 overall best weight: 0.1748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3348 Z= 0.123 Angle : 0.491 5.720 4557 Z= 0.254 Chirality : 0.042 0.138 478 Planarity : 0.003 0.026 587 Dihedral : 3.884 28.082 456 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.11 % Allowed : 10.73 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.25 (0.41), residues: 402 helix: -3.17 (0.74), residues: 31 sheet: 1.12 (0.46), residues: 145 loop : -0.57 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.001 0.000 HIS H 40 PHE 0.008 0.001 PHE A 377 TYR 0.009 0.001 TYR A 369 ARG 0.007 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 55 time to evaluate : 0.374 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 61 average time/residue: 0.1623 time to fit residues: 12.0504 Evaluate side-chains 62 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 35 optimal weight: 0.0970 chunk 21 optimal weight: 0.3980 chunk 15 optimal weight: 0.0030 chunk 27 optimal weight: 0.8980 chunk 10 optimal weight: 0.0050 chunk 31 optimal weight: 0.8980 overall best weight: 0.2402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3348 Z= 0.139 Angle : 0.505 7.078 4557 Z= 0.260 Chirality : 0.042 0.140 478 Planarity : 0.003 0.029 587 Dihedral : 3.814 25.197 456 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.39 % Allowed : 11.30 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.21 (0.41), residues: 402 helix: -3.10 (0.75), residues: 31 sheet: 1.14 (0.46), residues: 145 loop : -0.56 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.002 0.001 HIS H 101 PHE 0.007 0.001 PHE H 53 TYR 0.011 0.001 TYR H 91 ARG 0.006 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 54 time to evaluate : 0.379 Fit side-chains REVERT: L 17 ASP cc_start: 0.5696 (OUTLIER) cc_final: 0.4540 (t0) outliers start: 12 outliers final: 10 residues processed: 60 average time/residue: 0.1735 time to fit residues: 12.6566 Evaluate side-chains 65 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 54 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.0770 chunk 34 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 0.0570 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 35 optimal weight: 0.0000 chunk 30 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.3860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3348 Z= 0.185 Angle : 0.549 8.757 4557 Z= 0.283 Chirality : 0.043 0.138 478 Planarity : 0.004 0.031 587 Dihedral : 4.059 26.920 456 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.39 % Allowed : 10.73 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.25 (0.41), residues: 402 helix: -3.23 (0.74), residues: 31 sheet: 1.15 (0.46), residues: 145 loop : -0.59 (0.37), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.003 0.001 HIS H 101 PHE 0.009 0.001 PHE H 53 TYR 0.013 0.001 TYR H 91 ARG 0.006 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 54 time to evaluate : 0.396 Fit side-chains REVERT: L 17 ASP cc_start: 0.5653 (OUTLIER) cc_final: 0.4402 (t0) outliers start: 12 outliers final: 11 residues processed: 60 average time/residue: 0.1748 time to fit residues: 12.6695 Evaluate side-chains 65 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 53 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.0570 chunk 18 optimal weight: 0.0570 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 0.0770 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 31 optimal weight: 0.0870 overall best weight: 0.2352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3348 Z= 0.140 Angle : 0.519 9.266 4557 Z= 0.266 Chirality : 0.042 0.138 478 Planarity : 0.003 0.030 587 Dihedral : 3.884 25.319 456 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.82 % Allowed : 11.58 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.20 (0.41), residues: 402 helix: -3.14 (0.76), residues: 31 sheet: 1.17 (0.47), residues: 145 loop : -0.56 (0.37), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.002 0.001 HIS H 101 PHE 0.007 0.001 PHE H 53 TYR 0.010 0.001 TYR H 91 ARG 0.006 0.000 ARG A 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 0.389 Fit side-chains outliers start: 10 outliers final: 10 residues processed: 58 average time/residue: 0.1626 time to fit residues: 11.5970 Evaluate side-chains 62 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 52 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.0000 chunk 5 optimal weight: 0.3980 chunk 27 optimal weight: 0.0970 chunk 1 optimal weight: 0.1980 chunk 22 optimal weight: 0.0670 chunk 35 optimal weight: 0.0670 chunk 20 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 overall best weight: 0.0858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.146951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.125348 restraints weight = 5136.444| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.16 r_work: 0.3442 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 3348 Z= 0.112 Angle : 0.496 11.091 4557 Z= 0.249 Chirality : 0.041 0.136 478 Planarity : 0.003 0.027 587 Dihedral : 3.442 18.878 456 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.26 % Allowed : 12.15 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.41), residues: 402 helix: -3.06 (0.86), residues: 25 sheet: 1.37 (0.49), residues: 138 loop : -0.34 (0.36), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.001 0.000 HIS H 101 PHE 0.005 0.001 PHE A 490 TYR 0.008 0.001 TYR A 369 ARG 0.006 0.000 ARG A 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1491.85 seconds wall clock time: 28 minutes 21.05 seconds (1701.05 seconds total)