Starting phenix.real_space_refine on Fri Aug 2 14:52:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tma_41382/08_2024/8tma_41382.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tma_41382/08_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_41382/08_2024/8tma_41382.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tma_41382/08_2024/8tma_41382.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tma_41382/08_2024/8tma_41382.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tma_41382/08_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: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 3.99, per 1000 atoms: 1.23 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: 1.04 Conformation dependent library (CDL) restraints added in 752.8 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: 0.45 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: 0.88 Time building geometry restraints manager: 1.17 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 3.120 nonbonded pdb=" OE1 GLU A 406 " pdb=" NE2 GLN A 409 " model vdw 2.328 3.120 nonbonded pdb=" OG SER L 14 " pdb=" OD2 ASP L 17 " model vdw 2.345 3.040 nonbonded pdb=" OG SER A 349 " pdb=" O LEU A 452 " model vdw 2.380 3.040 nonbonded pdb=" NH2 ARG A 357 " pdb=" OD1 ASN A 394 " model vdw 2.394 3.120 ... (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 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: 3.470 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 15.690 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: 22.220 ------------------------------------------------------------------------------- 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 : 0.380 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: 0.1716 time to fit residues: 18.9740 Evaluate side-chains 58 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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: 1.9990 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 501 ASN H 6 GLN L 92 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 3348 Z= 0.397 Angle : 0.748 6.423 4557 Z= 0.395 Chirality : 0.051 0.169 478 Planarity : 0.005 0.034 587 Dihedral : 5.600 53.016 456 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.98 % Allowed : 7.34 % Favored : 90.68 % 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: -1.27 (0.40), residues: 402 helix: -4.05 (0.57), residues: 25 sheet: 0.70 (0.47), residues: 134 loop : -1.46 (0.35), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 96 HIS 0.004 0.002 HIS H 101 PHE 0.022 0.003 PHE H 29 TYR 0.021 0.002 TYR H 91 ARG 0.003 0.001 ARG L 18 *********************** 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 67 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: H 14 PRO cc_start: 0.5937 (Cg_endo) cc_final: 0.5725 (Cg_exo) outliers start: 7 outliers final: 7 residues processed: 63 average time/residue: 0.1680 time to fit residues: 12.8549 Evaluate side-chains 61 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 63 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 5 THR 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: 2.9990 chunk 29 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 0.0980 chunk 38 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3348 Z= 0.233 Angle : 0.605 5.549 4557 Z= 0.320 Chirality : 0.046 0.150 478 Planarity : 0.004 0.032 587 Dihedral : 5.190 52.470 456 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.11 % Allowed : 8.19 % Favored : 88.70 % 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: -1.05 (0.40), residues: 402 helix: -3.80 (0.68), residues: 25 sheet: 0.59 (0.46), residues: 144 loop : -1.22 (0.37), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.002 0.001 HIS H 40 PHE 0.012 0.002 PHE H 29 TYR 0.014 0.002 TYR H 91 ARG 0.002 0.000 ARG A 408 *********************** 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 70 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: H 14 PRO cc_start: 0.5810 (Cg_endo) cc_final: 0.5558 (Cg_exo) outliers start: 11 outliers final: 9 residues processed: 64 average time/residue: 0.1675 time to fit residues: 13.0165 Evaluate side-chains 65 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 21 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 16 optimal weight: 0.0770 chunk 23 optimal weight: 0.0070 chunk 35 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- 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: 0.8169 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3348 Z= 0.208 Angle : 0.572 5.172 4557 Z= 0.303 Chirality : 0.045 0.145 478 Planarity : 0.004 0.031 587 Dihedral : 4.839 43.796 456 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.11 % Allowed : 10.45 % 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: -0.72 (0.41), residues: 402 helix: -3.68 (0.74), residues: 25 sheet: 0.90 (0.45), residues: 145 loop : -1.05 (0.37), residues: 232 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 0.007 0.001 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: 11 poor density : 58 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 403 ARG cc_start: 0.8352 (ttp80) cc_final: 0.7885 (ttp80) REVERT: H 14 PRO cc_start: 0.5958 (Cg_endo) cc_final: 0.5742 (Cg_exo) outliers start: 11 outliers final: 9 residues processed: 64 average time/residue: 0.1670 time to fit residues: 13.0695 Evaluate side-chains 63 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 54 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 0.4980 chunk 7 optimal weight: 0.2980 chunk 22 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3348 Z= 0.241 Angle : 0.592 5.407 4557 Z= 0.311 Chirality : 0.045 0.150 478 Planarity : 0.004 0.031 587 Dihedral : 4.759 36.691 456 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % 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: -0.73 (0.41), residues: 402 helix: -3.66 (0.76), residues: 25 sheet: 0.60 (0.44), residues: 155 loop : -0.88 (0.38), residues: 222 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 0.011 0.001 PHE H 29 TYR 0.015 0.002 TYR H 91 ARG 0.004 0.000 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 68 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 56 time to evaluate : 0.400 Fit side-chains REVERT: H 14 PRO cc_start: 0.5836 (Cg_endo) cc_final: 0.5591 (Cg_exo) outliers start: 12 outliers final: 9 residues processed: 63 average time/residue: 0.1626 time to fit residues: 12.4926 Evaluate side-chains 64 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 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 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: 0.7980 chunk 37 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.2980 chunk 3 optimal weight: 0.0980 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 4 optimal weight: 0.0970 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 overall best weight: 0.3378 ------------------------------------------------------------------------------- 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: 0.8163 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3348 Z= 0.173 Angle : 0.535 5.412 4557 Z= 0.281 Chirality : 0.044 0.154 478 Planarity : 0.004 0.029 587 Dihedral : 4.457 32.347 456 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.67 % Allowed : 11.02 % 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: -0.59 (0.41), residues: 402 helix: -3.54 (0.81), residues: 25 sheet: 0.72 (0.45), residues: 155 loop : -0.81 (0.38), residues: 222 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 0.008 0.001 PHE A 377 TYR 0.012 0.001 TYR H 91 ARG 0.007 0.000 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 69 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 56 time to evaluate : 0.384 Fit side-chains REVERT: A 403 ARG cc_start: 0.8417 (ttp80) cc_final: 0.7807 (ttp80) REVERT: H 14 PRO cc_start: 0.5783 (Cg_endo) cc_final: 0.5565 (Cg_exo) outliers start: 13 outliers final: 9 residues processed: 64 average time/residue: 0.1587 time to fit residues: 12.4714 Evaluate side-chains 64 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 24 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 97 ILE 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: 0.3980 chunk 31 optimal weight: 0.8980 chunk 37 optimal weight: 0.2980 chunk 23 optimal weight: 0.0970 chunk 22 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 0.4980 chunk 7 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 0.2980 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3348 Z= 0.167 Angle : 0.541 5.814 4557 Z= 0.281 Chirality : 0.043 0.158 478 Planarity : 0.004 0.028 587 Dihedral : 4.264 29.170 456 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.39 % Allowed : 12.43 % Favored : 84.18 % 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: -0.53 (0.41), residues: 402 helix: -3.51 (0.81), residues: 25 sheet: 0.73 (0.45), residues: 155 loop : -0.75 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS H 101 PHE 0.008 0.001 PHE A 377 TYR 0.012 0.001 TYR H 91 ARG 0.005 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 68 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 56 time to evaluate : 0.397 Fit side-chains REVERT: A 403 ARG cc_start: 0.8456 (ttp80) cc_final: 0.7895 (ttp80) outliers start: 12 outliers final: 10 residues processed: 62 average time/residue: 0.1640 time to fit residues: 12.4983 Evaluate side-chains 65 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 24 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 97 ILE 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: 0.3980 chunk 29 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 27 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3348 Z= 0.248 Angle : 0.592 5.463 4557 Z= 0.311 Chirality : 0.045 0.162 478 Planarity : 0.004 0.033 587 Dihedral : 4.614 34.087 456 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.39 % Allowed : 12.15 % Favored : 84.46 % 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: -0.58 (0.41), residues: 402 helix: -3.52 (0.83), residues: 25 sheet: 0.71 (0.44), residues: 155 loop : -0.79 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.005 0.002 HIS H 101 PHE 0.011 0.001 PHE H 53 TYR 0.016 0.002 TYR H 91 ARG 0.005 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 67 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 55 time to evaluate : 0.383 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 61 average time/residue: 0.1765 time to fit residues: 13.0137 Evaluate side-chains 64 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 24 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 94 TYR 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: 1.9990 chunk 34 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 0.0040 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 38 optimal weight: 0.1980 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 3 optimal weight: 0.3980 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3348 Z= 0.210 Angle : 0.588 8.946 4557 Z= 0.305 Chirality : 0.044 0.156 478 Planarity : 0.004 0.030 587 Dihedral : 4.536 34.211 456 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.11 % Allowed : 12.15 % Favored : 84.75 % 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: -0.51 (0.41), residues: 402 helix: -3.48 (0.83), residues: 25 sheet: 0.76 (0.45), residues: 155 loop : -0.75 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.004 0.001 HIS H 101 PHE 0.009 0.001 PHE H 53 TYR 0.014 0.001 TYR H 91 ARG 0.006 0.000 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: 11 poor density : 55 time to evaluate : 0.381 Fit side-chains REVERT: A 403 ARG cc_start: 0.8490 (ttp80) cc_final: 0.7763 (ttp80) outliers start: 11 outliers final: 10 residues processed: 60 average time/residue: 0.1641 time to fit residues: 11.9783 Evaluate side-chains 65 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 24 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 94 TYR 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: 0.7980 chunk 18 optimal weight: 0.0270 chunk 24 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 0.0070 chunk 31 optimal weight: 0.7980 overall best weight: 0.4056 ------------------------------------------------------------------------------- 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: 0.8184 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3348 Z= 0.195 Angle : 0.552 5.385 4557 Z= 0.289 Chirality : 0.044 0.155 478 Planarity : 0.004 0.030 587 Dihedral : 4.473 33.820 456 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.67 % Allowed : 11.30 % Favored : 85.03 % 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: -0.46 (0.41), residues: 402 helix: -3.46 (0.84), residues: 25 sheet: 0.80 (0.45), residues: 155 loop : -0.72 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.004 0.001 HIS H 101 PHE 0.009 0.001 PHE H 53 TYR 0.013 0.001 TYR H 91 ARG 0.006 0.000 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 67 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 54 time to evaluate : 0.419 Fit side-chains REVERT: A 403 ARG cc_start: 0.8468 (ttp80) cc_final: 0.7717 (ttp80) REVERT: L 106 ILE cc_start: 0.7046 (OUTLIER) cc_final: 0.6842 (mt) outliers start: 13 outliers final: 10 residues processed: 61 average time/residue: 0.1681 time to fit residues: 12.5077 Evaluate side-chains 65 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 54 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 24 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 94 TYR 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: 0.6980 chunk 5 optimal weight: 0.1980 chunk 27 optimal weight: 0.7980 chunk 1 optimal weight: 0.1980 chunk 22 optimal weight: 0.0980 chunk 35 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 15 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.135476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.114280 restraints weight = 5144.281| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.02 r_work: 0.3278 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3348 Z= 0.178 Angle : 0.577 10.561 4557 Z= 0.297 Chirality : 0.043 0.154 478 Planarity : 0.004 0.028 587 Dihedral : 4.347 32.544 456 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.67 % Allowed : 11.30 % Favored : 85.03 % 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: -0.44 (0.41), residues: 402 helix: -3.40 (0.87), residues: 25 sheet: 0.82 (0.45), residues: 155 loop : -0.72 (0.37), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS H 101 PHE 0.008 0.001 PHE H 53 TYR 0.012 0.001 TYR H 91 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: 1423.60 seconds wall clock time: 25 minutes 49.80 seconds (1549.80 seconds total)