Starting phenix.real_space_refine on Tue Feb 11 10:41:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t32_25648/02_2025/7t32_25648.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t32_25648/02_2025/7t32_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/cci-nas-00/data/ceres_data/7t32_25648/02_2025/7t32_25648.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t32_25648/02_2025/7t32_25648.map" model { file = "/net/cci-nas-00/data/ceres_data/7t32_25648/02_2025/7t32_25648.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t32_25648/02_2025/7t32_25648.cif" } 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. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2861 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2836 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 375, 2830 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 10, 'TRANS': 364} 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: 375, 2830 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 10, 'TRANS': 364} 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: 2883 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'ZMA': 1} Classifications: {'undetermined': 1} 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: 3.86, per 1000 atoms: 1.35 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 662.9 milliseconds 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... Secondary structure from input PDB file: 14 helices and 0 sheets defined 90.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 8 through 33 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) removed outlier: 3.651A pdb=" N TRP A 32 " --> pdb=" O CYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 69 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 73 through 108 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 108 through 116 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 117 through 142 Proline residue: A 139 - end of helix removed outlier: 4.265A pdb=" N GLY A 142 " --> pdb=" O THR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 182 through 227 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 232 through 250 Processing helix chain 'A' and resid 268 through 289 removed outlier: 3.952A pdb=" N GLU A 289 " --> pdb=" O LYS A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 355 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 362 through 387 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 388 through 398 removed outlier: 3.856A pdb=" N THR A 394 " --> pdb=" O GLU A 390 " (cutoff:3.500A) 245 hydrogen bonds defined for protein. 735 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: 0.77 Time building geometry restraints manager: 0.90 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: 0.00 - 1.72: 3855 1.72 - 3.43: 104 3.43 - 5.15: 25 5.15 - 6.87: 8 6.87 - 8.58: 4 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: 3113 3.35 - 3.87: 4780 3.87 - 4.38: 4854 4.38 - 4.90: 8637 Nonbonded interactions: 22257 Sorted by model distance: nonbonded pdb=" NH1 ARG A 242 " pdb=" OD1 ASP A 281 " model vdw 2.313 3.120 nonbonded pdb=" O ALA A 231 " pdb=" N GLN A 233 " model vdw 2.321 3.120 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 3.120 nonbonded pdb=" O ALA A 134 " pdb=" OG1 THR A 138 " model vdw 2.363 3.040 ... (remaining 22252 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: 1.210 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.880 Find NCS groups from input model: 0.040 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.240 ------------------------------------------------------------------------------- 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= 0.388 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 to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.318 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1213 time to fit residues: 8.5347 Evaluate side-chains 49 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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: 0.9990 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.156146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.127268 restraints weight = 14878.729| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 9.46 r_work: 0.3396 rms_B_bonded: 8.17 restraints_weight: 2.0000 r_work: 0.3558 rms_B_bonded: 5.03 restraints_weight: 4.0000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3586 r_free = 0.3586 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 = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2925 Z= 0.225 Angle : 0.668 8.710 3996 Z= 0.343 Chirality : 0.041 0.167 480 Planarity : 0.005 0.061 496 Dihedral : 5.757 72.665 399 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.50 % Favored : 96.23 % Rotamer: Outliers : 0.70 % Allowed : 11.27 % Favored : 88.03 % 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: 2.17 (0.45), residues: 374 helix: 1.78 (0.30), residues: 320 sheet: None (None), residues: 0 loop : -0.48 (0.93), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 364 HIS 0.002 0.001 HIS A 374 PHE 0.015 0.001 PHE A 62 TYR 0.030 0.002 TYR A 9 ARG 0.001 0.000 ARG A 120 *********************** 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 59 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 289 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7749 (mp0) REVERT: A 291 LYS cc_start: 0.7298 (mttt) cc_final: 0.7046 (mttt) REVERT: A 368 LEU cc_start: 0.8191 (tp) cc_final: 0.7904 (tt) outliers start: 2 outliers final: 2 residues processed: 58 average time/residue: 0.1083 time to fit residues: 8.1136 Evaluate side-chains 53 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 224 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 1 optimal weight: 0.0470 chunk 12 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- 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 = 0.4090 r_free = 0.4090 target = 0.156014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.121680 restraints weight = 15928.334| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 7.70 r_work: 0.3438 rms_B_bonded: 7.23 restraints_weight: 2.0000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3424 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3424 r_free = 0.3424 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3424 r_free = 0.3424 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3424 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1705 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= 0.208 Angle : 0.643 6.568 3996 Z= 0.330 Chirality : 0.041 0.215 480 Planarity : 0.005 0.051 496 Dihedral : 5.524 66.217 399 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.23 % Favored : 96.50 % Rotamer: Outliers : 2.82 % Allowed : 13.73 % Favored : 83.45 % 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: 2.34 (0.45), residues: 374 helix: 1.90 (0.30), residues: 320 sheet: None (None), residues: 0 loop : -0.48 (0.94), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 364 HIS 0.001 0.000 HIS A 326 PHE 0.022 0.001 PHE A 182 TYR 0.020 0.002 TYR A 9 ARG 0.005 0.001 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 63 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 135 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7717 (mp) REVERT: A 219 ASN cc_start: 0.8787 (t0) cc_final: 0.8579 (m-40) REVERT: A 368 LEU cc_start: 0.8169 (tp) cc_final: 0.7942 (tt) REVERT: A 384 TYR cc_start: 0.8534 (m-80) cc_final: 0.8262 (m-10) outliers start: 8 outliers final: 5 residues processed: 62 average time/residue: 0.1048 time to fit residues: 8.4149 Evaluate side-chains 57 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 106 ILE 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 27 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.154865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.121073 restraints weight = 15233.860| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 7.53 r_work: 0.3416 rms_B_bonded: 7.06 restraints_weight: 2.0000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3408 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3408 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2925 Z= 0.246 Angle : 0.649 6.676 3996 Z= 0.332 Chirality : 0.040 0.165 480 Planarity : 0.004 0.047 496 Dihedral : 5.347 60.261 399 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.23 % Favored : 96.50 % Rotamer: Outliers : 3.17 % Allowed : 13.38 % Favored : 83.45 % 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: 2.30 (0.45), residues: 374 helix: 1.86 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.43 (0.97), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 364 HIS 0.002 0.001 HIS A 326 PHE 0.013 0.001 PHE A 62 TYR 0.019 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 65 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 135 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.7639 (mp) REVERT: A 219 ASN cc_start: 0.8805 (t0) cc_final: 0.8584 (m-40) REVERT: A 294 GLU cc_start: 0.7609 (mp0) cc_final: 0.7376 (mp0) REVERT: A 340 LEU cc_start: 0.8292 (tt) cc_final: 0.8063 (tp) REVERT: A 368 LEU cc_start: 0.8184 (tp) cc_final: 0.7956 (tt) outliers start: 9 outliers final: 5 residues processed: 63 average time/residue: 0.1046 time to fit residues: 8.5090 Evaluate side-chains 55 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4227 r_free = 0.4227 target = 0.161277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.134137 restraints weight = 14115.849| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 9.17 r_work: 0.3498 rms_B_bonded: 8.49 restraints_weight: 2.0000 r_work: 0.3662 rms_B_bonded: 5.22 restraints_weight: 4.0000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3680 r_free = 0.3680 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3680 r_free = 0.3680 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2925 Z= 0.227 Angle : 0.643 6.760 3996 Z= 0.331 Chirality : 0.041 0.226 480 Planarity : 0.004 0.043 496 Dihedral : 5.237 56.003 399 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.77 % Favored : 95.96 % Rotamer: Outliers : 2.82 % Allowed : 15.14 % Favored : 82.04 % 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: 2.39 (0.45), residues: 374 helix: 2.06 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -1.04 (0.92), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 364 HIS 0.001 0.000 HIS A 326 PHE 0.012 0.001 PHE A 62 TYR 0.018 0.002 TYR A 384 ARG 0.001 0.000 ARG A 396 *********************** 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 to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.7719 (t80) REVERT: A 135 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8132 (mp) REVERT: A 219 ASN cc_start: 0.8602 (t0) cc_final: 0.8366 (m-40) REVERT: A 291 LYS cc_start: 0.7049 (mtmt) cc_final: 0.6691 (mmtp) REVERT: A 294 GLU cc_start: 0.7329 (mp0) cc_final: 0.7074 (mp0) REVERT: A 340 LEU cc_start: 0.8329 (tt) cc_final: 0.8074 (tp) REVERT: A 368 LEU cc_start: 0.8199 (tp) cc_final: 0.7918 (tt) outliers start: 8 outliers final: 6 residues processed: 59 average time/residue: 0.1111 time to fit residues: 8.5441 Evaluate side-chains 60 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 106 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 226 GLU Chi-restraints excluded: chain A residue 352 THR 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 18 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4176 r_free = 0.4176 target = 0.158635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.124979 restraints weight = 15749.407| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 7.03 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3844 r_free = 0.3844 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3844 r_free = 0.3844 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2349 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= 0.215 Angle : 0.643 10.046 3996 Z= 0.325 Chirality : 0.040 0.194 480 Planarity : 0.004 0.041 496 Dihedral : 5.140 52.357 399 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.50 % Favored : 96.23 % Rotamer: Outliers : 3.17 % Allowed : 16.90 % Favored : 79.93 % 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: 2.54 (0.45), residues: 374 helix: 2.01 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.27 (0.99), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 364 HIS 0.001 0.000 HIS A 326 PHE 0.011 0.001 PHE A 62 TYR 0.016 0.001 TYR A 9 ARG 0.001 0.000 ARG A 270 *********************** 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 66 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8682 (mp) cc_final: 0.8481 (mp) REVERT: A 133 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.7680 (t80) REVERT: A 135 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8148 (mp) REVERT: A 219 ASN cc_start: 0.8134 (t0) cc_final: 0.7918 (m-40) REVERT: A 368 LEU cc_start: 0.8311 (tp) cc_final: 0.8026 (tt) outliers start: 9 outliers final: 7 residues processed: 64 average time/residue: 0.1063 time to fit residues: 8.7955 Evaluate side-chains 61 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 106 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 226 GLU 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 16 optimal weight: 0.0670 chunk 20 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 chunk 35 optimal weight: 0.8980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 = 0.4194 r_free = 0.4194 target = 0.160145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.126493 restraints weight = 21465.068| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 8.10 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3847 r_free = 0.3847 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3847 r_free = 0.3847 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2925 Z= 0.203 Angle : 0.647 9.556 3996 Z= 0.326 Chirality : 0.040 0.216 480 Planarity : 0.004 0.039 496 Dihedral : 5.029 49.652 399 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.77 % Favored : 95.96 % Rotamer: Outliers : 3.52 % Allowed : 16.90 % 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: 2.63 (0.45), residues: 374 helix: 2.09 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.38 (0.95), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 364 HIS 0.001 0.000 HIS A 155 PHE 0.011 0.001 PHE A 62 TYR 0.017 0.001 TYR A 9 ARG 0.001 0.000 ARG A 387 *********************** 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 67 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8646 (mp) cc_final: 0.8407 (mp) REVERT: A 133 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.7773 (t80) REVERT: A 135 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8211 (mp) REVERT: A 219 ASN cc_start: 0.8040 (t0) cc_final: 0.7835 (m-40) REVERT: A 368 LEU cc_start: 0.8331 (tp) cc_final: 0.8048 (tt) outliers start: 10 outliers final: 7 residues processed: 64 average time/residue: 0.1202 time to fit residues: 9.8990 Evaluate side-chains 63 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 106 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 226 GLU Chi-restraints excluded: chain A residue 352 THR 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 23 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 0.0470 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.164251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.137424 restraints weight = 10853.666| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 7.92 r_work: 0.3651 rms_B_bonded: 7.70 restraints_weight: 2.0000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3609 r_free = 0.3609 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3609 r_free = 0.3609 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2925 Z= 0.207 Angle : 0.643 9.752 3996 Z= 0.327 Chirality : 0.040 0.239 480 Planarity : 0.004 0.039 496 Dihedral : 5.000 48.191 399 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.23 % Favored : 96.50 % Rotamer: Outliers : 3.87 % Allowed : 17.61 % Favored : 78.52 % 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: 2.61 (0.45), residues: 374 helix: 2.10 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.60 (0.90), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 364 HIS 0.001 0.000 HIS A 75 PHE 0.017 0.001 PHE A 182 TYR 0.015 0.002 TYR A 9 ARG 0.001 0.000 ARG A 270 *********************** 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 67 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.328 Fit side-chains REVERT: A 19 LEU cc_start: 0.8667 (mp) cc_final: 0.8437 (mp) REVERT: A 103 TYR cc_start: 0.8165 (t80) cc_final: 0.7943 (t80) REVERT: A 133 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.7736 (t80) REVERT: A 135 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8081 (mp) REVERT: A 167 LEU cc_start: 0.8941 (tp) cc_final: 0.8506 (tt) REVERT: A 219 ASN cc_start: 0.8763 (t0) cc_final: 0.8526 (m-40) REVERT: A 226 GLU cc_start: 0.6411 (OUTLIER) cc_final: 0.6114 (mp0) REVERT: A 368 LEU cc_start: 0.8170 (tp) cc_final: 0.7916 (tt) outliers start: 11 outliers final: 7 residues processed: 64 average time/residue: 0.1321 time to fit residues: 11.6299 Evaluate side-chains 64 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 106 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 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 14 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 36 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 0.1980 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 5 optimal weight: 0.0070 chunk 24 optimal weight: 2.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- 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 = 0.4251 r_free = 0.4251 target = 0.164183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.137557 restraints weight = 14888.653| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 9.36 r_work: 0.3555 rms_B_bonded: 8.85 restraints_weight: 2.0000 r_work: 0.3721 rms_B_bonded: 5.40 restraints_weight: 4.0000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3741 r_free = 0.3741 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3741 r_free = 0.3741 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2736 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= 0.199 Angle : 0.636 9.642 3996 Z= 0.324 Chirality : 0.040 0.203 480 Planarity : 0.004 0.038 496 Dihedral : 4.946 45.809 399 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.23 % Favored : 96.50 % Rotamer: Outliers : 3.87 % Allowed : 17.25 % 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: 2.68 (0.45), residues: 374 helix: 2.18 (0.30), residues: 320 sheet: None (None), residues: 0 loop : -0.73 (0.88), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 364 HIS 0.001 0.000 HIS A 374 PHE 0.011 0.001 PHE A 62 TYR 0.015 0.002 TYR A 9 ARG 0.001 0.000 ARG A 387 *********************** 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 68 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.313 Fit side-chains REVERT: A 19 LEU cc_start: 0.8599 (mp) cc_final: 0.8371 (mp) REVERT: A 133 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.7786 (t80) REVERT: A 135 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8184 (mp) REVERT: A 167 LEU cc_start: 0.8913 (tp) cc_final: 0.8487 (tt) REVERT: A 219 ASN cc_start: 0.8573 (t0) cc_final: 0.8330 (m-40) REVERT: A 226 GLU cc_start: 0.6168 (OUTLIER) cc_final: 0.5950 (mp0) REVERT: A 368 LEU cc_start: 0.8113 (tp) cc_final: 0.7829 (tt) outliers start: 11 outliers final: 7 residues processed: 64 average time/residue: 0.1095 time to fit residues: 8.9767 Evaluate side-chains 64 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 106 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 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 23 optimal weight: 0.4980 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 chunk 28 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 21 optimal weight: 0.0370 chunk 31 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 26 optimal weight: 0.0170 overall best weight: 0.3696 ------------------------------------------------------------------------------- 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 = 0.4255 r_free = 0.4255 target = 0.164469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.138194 restraints weight = 15607.035| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 9.66 r_work: 0.3545 rms_B_bonded: 9.20 restraints_weight: 2.0000 r_work: 0.3713 rms_B_bonded: 5.61 restraints_weight: 4.0000 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3733 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3733 r_free = 0.3733 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3733 r_free = 0.3733 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3733 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2925 Z= 0.201 Angle : 0.638 9.613 3996 Z= 0.324 Chirality : 0.040 0.235 480 Planarity : 0.004 0.038 496 Dihedral : 4.948 44.896 399 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.23 % Favored : 96.50 % Rotamer: Outliers : 3.17 % Allowed : 18.31 % Favored : 78.52 % 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: 2.69 (0.45), residues: 374 helix: 2.16 (0.30), residues: 322 sheet: None (None), residues: 0 loop : -0.61 (0.90), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 364 HIS 0.001 0.000 HIS A 75 PHE 0.019 0.001 PHE A 182 TYR 0.015 0.001 TYR A 9 ARG 0.001 0.000 ARG A 242 ********************** 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 65 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.314 Fit side-chains REVERT: A 19 LEU cc_start: 0.8602 (mp) cc_final: 0.8383 (mp) REVERT: A 103 TYR cc_start: 0.7987 (t80) cc_final: 0.7787 (t80) REVERT: A 133 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.7653 (t80) REVERT: A 135 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8155 (mp) REVERT: A 167 LEU cc_start: 0.8877 (tp) cc_final: 0.8435 (tt) REVERT: A 219 ASN cc_start: 0.8607 (t0) cc_final: 0.8358 (m-40) REVERT: A 226 GLU cc_start: 0.6221 (OUTLIER) cc_final: 0.5991 (mp0) REVERT: A 368 LEU cc_start: 0.8089 (tp) cc_final: 0.7816 (tt) outliers start: 9 outliers final: 6 residues processed: 62 average time/residue: 0.1026 time to fit residues: 8.3462 Evaluate side-chains 61 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 106 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 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 27 optimal weight: 0.3980 chunk 0 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 16 optimal weight: 0.0970 chunk 4 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4247 r_free = 0.4247 target = 0.163667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.136740 restraints weight = 12347.779| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 7.69 r_work: 0.3572 rms_B_bonded: 7.45 restraints_weight: 2.0000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3580 r_free = 0.3580 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3580 r_free = 0.3580 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2925 Z= 0.235 Angle : 0.655 9.737 3996 Z= 0.332 Chirality : 0.041 0.213 480 Planarity : 0.004 0.040 496 Dihedral : 4.965 45.887 399 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.96 % Favored : 96.77 % Rotamer: Outliers : 3.52 % Allowed : 18.66 % Favored : 77.82 % 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: 2.61 (0.45), residues: 374 helix: 2.13 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.78 (0.87), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 364 HIS 0.001 0.000 HIS A 75 PHE 0.010 0.001 PHE A 62 TYR 0.015 0.001 TYR A 384 ARG 0.001 0.000 ARG A 396 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2157.36 seconds wall clock time: 38 minutes 41.67 seconds (2321.67 seconds total)