Starting phenix.real_space_refine on Sun Mar 10 22:32:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t32_25648/03_2024/7t32_25648_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t32_25648/03_2024/7t32_25648.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t32_25648/03_2024/7t32_25648.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t32_25648/03_2024/7t32_25648.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t32_25648/03_2024/7t32_25648_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t32_25648/03_2024/7t32_25648_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2829 atoms to isotropic. 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 19 5.16 5 C 1874 2.51 5 N 473 2.21 5 O 495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 169": "OE1" <-> "OE2" Residue "A TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A ASP 282": "OD1" <-> "OD2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "A TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2861 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2861 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 376, 2855 Unusual residues: {'ZMA': 1} Classifications: {'peptide': 375, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 10, 'TRANS': 364, None: 1} Not linked: pdbres="ILE A 398 " pdbres="ZMA A1201 " Chain breaks: 1 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 66 Conformer: "B" Number of residues, atoms: 376, 2855 Unusual residues: {'ZMA': 1} Classifications: {'peptide': 375, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 10, 'TRANS': 364, None: 1} Not linked: pdbres="ILE A 398 " pdbres="ZMA A1201 " Chain breaks: 1 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 66 bond proxies already assigned to first conformer: 2911 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER A 35 " occ=0.60 ... (10 atoms not shown) pdb=" OG BSER A 35 " occ=0.40 Time building chain proxies: 3.41, per 1000 atoms: 1.19 Number of scatterers: 2861 At special positions: 0 Unit cell: (55.945, 78.49, 109.385, 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 19 16.00 O 495 8.00 N 473 7.00 C 1874 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 146 " distance=2.03 Simple disulfide: pdb=" SG CYS A 77 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 358 " distance=2.03 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: 1.24 Conformation dependent library (CDL) restraints added in 1.1 seconds 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 714 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 13 helices and 0 sheets defined 83.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 9 through 30 removed outlier: 3.556A pdb=" N LEU A 19 " --> pdb=" O ALA A 15 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL A 27 " --> pdb=" O GLY A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 68 removed outlier: 4.551A pdb=" N ILE A 60 " --> pdb=" O GLY A 56 " (cutoff:3.500A) Proline residue: A 61 - end of helix removed outlier: 4.007A pdb=" N THR A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 107 removed outlier: 4.849A pdb=" N VAL A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 115 removed outlier: 4.722A pdb=" N ASN A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N GLY A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 141 Proline residue: A 139 - end of helix Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 168 through 171 No H-bonds generated for 'chain 'A' and resid 168 through 171' Processing helix chain 'A' and resid 174 through 226 removed outlier: 4.249A pdb=" N PHE A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A 183 " --> pdb=" O TYR A 179 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A 184 " --> pdb=" O PHE A 180 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N CYS A 185 " --> pdb=" O ASN A 181 " (cutoff:3.500A) Proline residue: A 189 - end of helix removed outlier: 4.096A pdb=" N LEU A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 249 Processing helix chain 'A' and resid 268 through 288 Processing helix chain 'A' and resid 292 through 354 removed outlier: 3.987A pdb=" N THR A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR A 305 " --> pdb=" O GLN A 301 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 319 " --> pdb=" O GLU A 315 " (cutoff:3.500A) Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 363 through 386 removed outlier: 3.661A pdb=" N ASN A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N SER A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN A 380 " --> pdb=" O ASN A 376 " (cutoff:3.500A) Proline residue: A 381 - end of helix Processing helix chain 'A' and resid 389 through 397 removed outlier: 3.856A pdb=" N THR A 394 " --> pdb=" O GLU A 390 " (cutoff:3.500A) 221 hydrogen bonds defined for protein. 663 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: 0.78 Time building geometry restraints manager: 1.34 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: 886 1.34 - 1.46: 408 1.46 - 1.57: 1606 1.57 - 1.69: 0 1.69 - 1.81: 25 Bond restraints: 2925 Sorted by residual: bond pdb=" C14 ZMA A1201 " pdb=" N15 ZMA A1201 " ideal model delta sigma weight residual 1.321 1.450 -0.129 2.00e-02 2.50e+03 4.16e+01 bond pdb=" C11 ZMA A1201 " pdb=" N10 ZMA A1201 " ideal model delta sigma weight residual 1.334 1.453 -0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" C20 ZMA A1201 " pdb=" C21 ZMA A1201 " ideal model delta sigma weight residual 1.442 1.526 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" C18 ZMA A1201 " pdb=" N16 ZMA A1201 " ideal model delta sigma weight residual 1.372 1.294 0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" C18 ZMA A1201 " pdb=" N19 ZMA A1201 " ideal model delta sigma weight residual 1.320 1.388 -0.068 2.00e-02 2.50e+03 1.14e+01 ... (remaining 2920 not shown) Histogram of bond angle deviations from ideal: 100.36 - 107.09: 62 107.09 - 113.82: 1688 113.82 - 120.55: 1210 120.55 - 127.28: 1005 127.28 - 134.01: 31 Bond angle restraints: 3996 Sorted by residual: angle pdb=" N VAL A 171 " pdb=" CA VAL A 171 " pdb=" C VAL A 171 " ideal model delta sigma weight residual 113.53 109.69 3.84 9.80e-01 1.04e+00 1.54e+01 angle pdb=" N GLU A 226 " pdb=" CA GLU A 226 " pdb=" CB GLU A 226 " ideal model delta sigma weight residual 110.28 116.02 -5.74 1.55e+00 4.16e-01 1.37e+01 angle pdb=" N VAL A 31 " pdb=" CA VAL A 31 " pdb=" C VAL A 31 " ideal model delta sigma weight residual 113.00 108.85 4.15 1.30e+00 5.92e-01 1.02e+01 angle pdb=" CA GLU A 226 " pdb=" CB GLU A 226 " pdb=" CG GLU A 226 " ideal model delta sigma weight residual 114.10 120.49 -6.39 2.00e+00 2.50e-01 1.02e+01 angle pdb=" C ASP A 229 " pdb=" N ASN A 230 " pdb=" CA ASN A 230 " ideal model delta sigma weight residual 121.54 127.48 -5.94 1.91e+00 2.74e-01 9.68e+00 ... (remaining 3991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.31: 1523 16.31 - 32.61: 136 32.61 - 48.92: 32 48.92 - 65.23: 12 65.23 - 81.54: 2 Dihedral angle restraints: 1705 sinusoidal: 604 harmonic: 1101 Sorted by residual: dihedral pdb=" CB CYS A 77 " pdb=" SG CYS A 77 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual 93.00 160.63 -67.63 1 1.00e+01 1.00e-02 5.95e+01 dihedral pdb=" CA PHE A 182 " pdb=" C PHE A 182 " pdb=" N PHE A 183 " pdb=" CA PHE A 183 " ideal model delta harmonic sigma weight residual -180.00 -160.03 -19.97 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA CYS A 185 " pdb=" C CYS A 185 " pdb=" N VAL A 186 " pdb=" CA VAL A 186 " ideal model delta harmonic sigma weight residual 180.00 163.99 16.01 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 1702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 315 0.030 - 0.060: 106 0.060 - 0.090: 40 0.090 - 0.120: 16 0.120 - 0.150: 3 Chirality restraints: 480 Sorted by residual: chirality pdb=" CA GLU A 226 " pdb=" N GLU A 226 " pdb=" C GLU A 226 " pdb=" CB GLU A 226 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.62e-01 chirality pdb=" CA ASN A 230 " pdb=" N ASN A 230 " pdb=" C ASN A 230 " pdb=" CB ASN A 230 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA GLN A 157 " pdb=" N GLN A 157 " pdb=" C GLN A 157 " pdb=" CB GLN A 157 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 477 not shown) Planarity restraints: 496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 188 " -0.049 5.00e-02 4.00e+02 7.44e-02 8.86e+00 pdb=" N PRO A 189 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 189 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 189 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 148 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO A 149 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 149 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 149 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 307 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.82e+00 pdb=" C ASN A 307 " -0.034 2.00e-02 2.50e+03 pdb=" O ASN A 307 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA A 308 " 0.011 2.00e-02 2.50e+03 ... (remaining 493 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 873 2.83 - 3.35: 3135 3.35 - 3.87: 4812 3.87 - 4.38: 4892 4.38 - 4.90: 8641 Nonbonded interactions: 22353 Sorted by model distance: nonbonded pdb=" NH1 ARG A 242 " pdb=" OD1 ASP A 281 " model vdw 2.313 2.520 nonbonded pdb=" O ALA A 231 " pdb=" N GLN A 233 " model vdw 2.321 2.520 nonbonded pdb=" O LEU A 222 " pdb=" OE1 GLU A 226 " model vdw 2.341 3.040 nonbonded pdb=" N GLU A 294 " pdb=" OE1 GLU A 294 " model vdw 2.359 2.520 nonbonded pdb=" O ALA A 134 " pdb=" OG1 THR A 138 " model vdw 2.363 2.440 ... (remaining 22348 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=0.40 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 5.560 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.730 Find NCS groups from input model: 0.080 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 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 : 0.006 0.129 2925 Z= 0.418 Angle : 0.774 8.585 3996 Z= 0.419 Chirality : 0.039 0.150 480 Planarity : 0.005 0.074 496 Dihedral : 14.073 81.537 982 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.12 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.86 (0.45), residues: 374 helix: 1.56 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -0.32 (0.88), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 364 HIS 0.002 0.001 HIS A 155 PHE 0.018 0.001 PHE A 395 TYR 0.008 0.001 TYR A 384 ARG 0.002 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.353 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1208 time to fit residues: 8.5085 Evaluate side-chains 49 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 0.1980 chunk 17 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2925 Z= 0.269 Angle : 0.659 8.547 3996 Z= 0.331 Chirality : 0.040 0.152 480 Planarity : 0.005 0.062 496 Dihedral : 5.761 66.931 399 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.04 % Favored : 95.69 % Rotamer: Outliers : 1.41 % Allowed : 11.62 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.10 (0.45), residues: 374 helix: 1.74 (0.30), residues: 318 sheet: None (None), residues: 0 loop : -0.50 (0.93), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 364 HIS 0.002 0.001 HIS A 326 PHE 0.014 0.001 PHE A 62 TYR 0.034 0.002 TYR A 9 ARG 0.002 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 135 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8132 (mp) REVERT: A 289 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7401 (mp0) REVERT: A 368 LEU cc_start: 0.8302 (tp) cc_final: 0.8002 (tt) outliers start: 4 outliers final: 3 residues processed: 59 average time/residue: 0.1005 time to fit residues: 7.6805 Evaluate side-chains 55 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 352 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 18 optimal weight: 0.2980 chunk 10 optimal weight: 0.3980 chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 0.0270 chunk 36 optimal weight: 0.2980 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 326 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2925 Z= 0.186 Angle : 0.601 7.112 3996 Z= 0.303 Chirality : 0.039 0.218 480 Planarity : 0.004 0.051 496 Dihedral : 5.450 59.488 399 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.31 % Favored : 95.42 % Rotamer: Outliers : 1.76 % Allowed : 15.14 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.35 (0.45), residues: 374 helix: 1.89 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -0.30 (0.92), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 364 HIS 0.001 0.000 HIS A 374 PHE 0.013 0.001 PHE A 62 TYR 0.023 0.002 TYR A 9 ARG 0.001 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 368 LEU cc_start: 0.8289 (tp) cc_final: 0.7997 (tt) outliers start: 5 outliers final: 3 residues processed: 59 average time/residue: 0.1028 time to fit residues: 7.9205 Evaluate side-chains 53 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 133 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.7980 chunk 16 optimal weight: 0.2980 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7449 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2925 Z= 0.214 Angle : 0.613 6.854 3996 Z= 0.306 Chirality : 0.040 0.215 480 Planarity : 0.004 0.047 496 Dihedral : 5.381 56.690 399 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.04 % Favored : 95.69 % Rotamer: Outliers : 2.46 % Allowed : 16.20 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.43 (0.45), residues: 374 helix: 1.95 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -0.32 (0.93), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 364 HIS 0.001 0.000 HIS A 346 PHE 0.012 0.001 PHE A 395 TYR 0.020 0.002 TYR A 9 ARG 0.001 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 135 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8167 (mp) REVERT: A 368 LEU cc_start: 0.8297 (tp) cc_final: 0.7966 (tt) REVERT: A 395 PHE cc_start: 0.6330 (m-80) cc_final: 0.5929 (m-10) outliers start: 7 outliers final: 4 residues processed: 63 average time/residue: 0.1071 time to fit residues: 8.7345 Evaluate side-chains 56 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 224 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.0670 chunk 14 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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: 0.7432 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2925 Z= 0.200 Angle : 0.595 7.092 3996 Z= 0.299 Chirality : 0.039 0.211 480 Planarity : 0.004 0.044 496 Dihedral : 5.272 54.090 399 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.31 % Favored : 95.42 % Rotamer: Outliers : 2.11 % Allowed : 16.90 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.50 (0.46), residues: 374 helix: 2.00 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -0.29 (0.95), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 364 HIS 0.001 0.000 HIS A 75 PHE 0.010 0.001 PHE A 62 TYR 0.019 0.001 TYR A 9 ARG 0.001 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.333 Fit side-chains REVERT: A 135 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.7906 (mp) REVERT: A 216 GLU cc_start: 0.6927 (mm-30) cc_final: 0.6718 (mm-30) REVERT: A 226 GLU cc_start: 0.6677 (mp0) cc_final: 0.6368 (mp0) REVERT: A 340 LEU cc_start: 0.8192 (tt) cc_final: 0.7970 (tp) REVERT: A 368 LEU cc_start: 0.8282 (tp) cc_final: 0.7955 (tt) outliers start: 6 outliers final: 5 residues processed: 61 average time/residue: 0.1130 time to fit residues: 8.9635 Evaluate side-chains 60 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 365 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.7475 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2925 Z= 0.229 Angle : 0.613 6.952 3996 Z= 0.310 Chirality : 0.040 0.205 480 Planarity : 0.004 0.043 496 Dihedral : 5.268 53.091 399 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.04 % Favored : 95.69 % Rotamer: Outliers : 2.82 % Allowed : 17.61 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.41 (0.45), residues: 374 helix: 1.94 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -0.33 (0.94), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 364 HIS 0.001 0.000 HIS A 75 PHE 0.011 0.001 PHE A 62 TYR 0.018 0.002 TYR A 9 ARG 0.001 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.7581 (t80) REVERT: A 135 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8217 (mp) REVERT: A 340 LEU cc_start: 0.8179 (tt) cc_final: 0.7973 (tp) REVERT: A 368 LEU cc_start: 0.8292 (tp) cc_final: 0.7971 (tt) outliers start: 8 outliers final: 5 residues processed: 62 average time/residue: 0.1025 time to fit residues: 8.4282 Evaluate side-chains 60 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 53 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 365 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 20.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7463 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2925 Z= 0.217 Angle : 0.610 6.970 3996 Z= 0.309 Chirality : 0.040 0.227 480 Planarity : 0.004 0.042 496 Dihedral : 5.226 51.820 399 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.31 % Favored : 95.42 % Rotamer: Outliers : 2.46 % Allowed : 18.66 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.42 (0.45), residues: 374 helix: 1.97 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -0.46 (0.92), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 364 HIS 0.001 0.000 HIS A 374 PHE 0.024 0.001 PHE A 182 TYR 0.017 0.001 TYR A 9 ARG 0.001 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 13 GLU cc_start: 0.9030 (tp30) cc_final: 0.8827 (tp30) REVERT: A 133 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.7599 (t80) REVERT: A 135 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8315 (mp) REVERT: A 340 LEU cc_start: 0.8191 (tt) cc_final: 0.7989 (tp) REVERT: A 368 LEU cc_start: 0.8192 (tp) cc_final: 0.7873 (tt) outliers start: 7 outliers final: 5 residues processed: 60 average time/residue: 0.1006 time to fit residues: 8.0408 Evaluate side-chains 60 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 53 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 365 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 14 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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: 0.7464 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2925 Z= 0.215 Angle : 0.621 10.183 3996 Z= 0.310 Chirality : 0.040 0.224 480 Planarity : 0.004 0.041 496 Dihedral : 5.221 51.113 399 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.04 % Favored : 95.69 % Rotamer: Outliers : 3.17 % Allowed : 18.66 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.41 (0.45), residues: 374 helix: 1.99 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -0.74 (0.87), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 364 HIS 0.001 0.000 HIS A 75 PHE 0.022 0.001 PHE A 182 TYR 0.017 0.001 TYR A 9 ARG 0.001 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 54 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.7562 (t80) REVERT: A 135 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8404 (mp) REVERT: A 340 LEU cc_start: 0.8173 (tt) cc_final: 0.7971 (tp) REVERT: A 368 LEU cc_start: 0.8189 (tp) cc_final: 0.7877 (tt) outliers start: 9 outliers final: 7 residues processed: 60 average time/residue: 0.0993 time to fit residues: 7.8231 Evaluate side-chains 62 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 365 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7460 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2925 Z= 0.213 Angle : 0.626 9.870 3996 Z= 0.312 Chirality : 0.040 0.220 480 Planarity : 0.004 0.040 496 Dihedral : 5.209 50.403 399 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.58 % Favored : 95.15 % Rotamer: Outliers : 3.17 % Allowed : 19.37 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.41 (0.45), residues: 374 helix: 2.04 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -1.05 (0.86), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 364 HIS 0.001 0.000 HIS A 346 PHE 0.021 0.001 PHE A 182 TYR 0.018 0.001 TYR A 9 ARG 0.001 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.7522 (t80) REVERT: A 135 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8464 (mp) REVERT: A 169 GLU cc_start: 0.8315 (pm20) cc_final: 0.7751 (tp30) REVERT: A 340 LEU cc_start: 0.8176 (tt) cc_final: 0.7967 (tp) REVERT: A 368 LEU cc_start: 0.8184 (tp) cc_final: 0.7878 (tt) outliers start: 9 outliers final: 7 residues processed: 62 average time/residue: 0.1037 time to fit residues: 8.5147 Evaluate side-chains 63 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 54 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 365 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7477 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2925 Z= 0.229 Angle : 0.637 9.933 3996 Z= 0.316 Chirality : 0.040 0.223 480 Planarity : 0.004 0.040 496 Dihedral : 5.171 50.051 399 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.58 % Favored : 95.15 % Rotamer: Outliers : 3.17 % Allowed : 19.37 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.36 (0.44), residues: 374 helix: 2.02 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -1.11 (0.85), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 364 HIS 0.001 0.000 HIS A 374 PHE 0.023 0.001 PHE A 182 TYR 0.017 0.001 TYR A 9 ARG 0.001 0.000 ARG A 306 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.7623 (t80) REVERT: A 135 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8520 (mp) REVERT: A 340 LEU cc_start: 0.8180 (tt) cc_final: 0.7979 (tp) REVERT: A 368 LEU cc_start: 0.8171 (tp) cc_final: 0.7879 (tt) outliers start: 9 outliers final: 7 residues processed: 59 average time/residue: 0.0990 time to fit residues: 7.7460 Evaluate side-chains 62 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 365 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 0.2980 chunk 25 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 0.2980 chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 20.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4187 r_free = 0.4187 target = 0.159527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.131394 restraints weight = 19033.033| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 10.91 r_work: 0.3469 rms_B_bonded: 9.66 restraints_weight: 2.0000 r_work: 0.3640 rms_B_bonded: 5.95 restraints_weight: 4.0000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2925 Z= 0.207 Angle : 0.628 10.245 3996 Z= 0.311 Chirality : 0.040 0.228 480 Planarity : 0.004 0.039 496 Dihedral : 5.130 48.848 399 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.85 % Favored : 94.88 % Rotamer: Outliers : 3.17 % Allowed : 19.37 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.41 (0.45), residues: 374 helix: 2.07 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -1.22 (0.84), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 364 HIS 0.001 0.000 HIS A 374 PHE 0.021 0.001 PHE A 182 TYR 0.017 0.001 TYR A 9 ARG 0.001 0.000 ARG A 306 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1165.00 seconds wall clock time: 21 minutes 30.38 seconds (1290.38 seconds total)