Starting phenix.real_space_refine on Thu Mar 6 07:18:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t32_25648/03_2025/7t32_25648.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t32_25648/03_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_25648/03_2025/7t32_25648.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t32_25648/03_2025/7t32_25648.map" model { file = "/net/cci-nas-00/data/ceres_data/7t32_25648/03_2025/7t32_25648.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t32_25648/03_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-5624/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: 4.20, per 1000 atoms: 1.47 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: 0.78 Conformation dependent library (CDL) restraints added in 710.1 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: 0.74 Time building geometry restraints manager: 0.89 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: 2.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.300 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.040 ------------------------------------------------------------------------------- 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 : 0.280 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1171 time to fit residues: 8.2401 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 : 0.307 ------------------------------------------------------------------------------- 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: 0.3398 rms_B_bonded: 8.14 restraints_weight: 2.0000 r_work: 0.3557 rms_B_bonded: 5.04 restraints_weight: 4.0000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3585 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3585 r_free = 0.3585 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 = 0.3585 r_free = 0.3585 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3585 ------------------------------------------------------------------------------- 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 : 0.272 Fit side-chains revert: symmetry clash REVERT: A 289 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7750 (mp0) REVERT: A 291 LYS cc_start: 0.7298 (mttt) cc_final: 0.7047 (mttt) REVERT: A 368 LEU cc_start: 0.8192 (tp) cc_final: 0.7904 (tt) outliers start: 2 outliers final: 2 residues processed: 58 average time/residue: 0.1053 time to fit residues: 7.9562 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 : 0.312 ------------------------------------------------------------------------------- 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: 0.1980 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 = 0.4198 r_free = 0.4198 target = 0.161199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.133200 restraints weight = 15981.883| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 9.85 r_work: 0.3529 rms_B_bonded: 8.46 restraints_weight: 2.0000 r_work: 0.3693 rms_B_bonded: 5.18 restraints_weight: 4.0000 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3708 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3708 r_free = 0.3708 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3708 r_free = 0.3708 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1751 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= 0.194 Angle : 0.632 6.890 3996 Z= 0.324 Chirality : 0.041 0.228 480 Planarity : 0.005 0.051 496 Dihedral : 5.463 64.528 399 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.50 % Favored : 96.23 % Rotamer: Outliers : 2.46 % Allowed : 14.08 % 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: 2.38 (0.45), residues: 374 helix: 1.94 (0.30), residues: 320 sheet: None (None), residues: 0 loop : -0.51 (0.93), 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 155 PHE 0.021 0.001 PHE A 182 TYR 0.020 0.002 TYR A 9 ARG 0.003 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 64 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 135 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.7866 (mp) REVERT: A 219 ASN cc_start: 0.8628 (t0) cc_final: 0.8399 (m-40) REVERT: A 289 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7814 (mp0) REVERT: A 368 LEU cc_start: 0.8217 (tp) cc_final: 0.7932 (tt) REVERT: A 384 TYR cc_start: 0.8431 (m-80) cc_final: 0.8204 (m-10) outliers start: 7 outliers final: 4 residues processed: 63 average time/residue: 0.1038 time to fit residues: 8.4852 Evaluate side-chains 59 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 352 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 27 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 18 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 6 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.157236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.122063 restraints weight = 15175.800| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 7.47 r_work: 0.3428 rms_B_bonded: 7.01 restraints_weight: 2.0000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3443 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3443 r_free = 0.3443 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3443 r_free = 0.3443 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3443 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2018 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= 0.221 Angle : 0.639 6.677 3996 Z= 0.323 Chirality : 0.041 0.201 480 Planarity : 0.004 0.047 496 Dihedral : 5.324 59.993 399 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.23 % Favored : 96.50 % Rotamer: Outliers : 3.52 % Allowed : 13.38 % 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: 2.33 (0.45), residues: 374 helix: 1.88 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.41 (0.96), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 364 HIS 0.002 0.000 HIS A 326 PHE 0.029 0.002 PHE A 180 TYR 0.017 0.002 TYR A 9 ARG 0.002 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 68 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: A 135 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7491 (mp) REVERT: A 219 ASN cc_start: 0.8729 (t0) cc_final: 0.8496 (m-40) REVERT: A 340 LEU cc_start: 0.8222 (tt) cc_final: 0.7976 (tp) REVERT: A 368 LEU cc_start: 0.8181 (tp) cc_final: 0.7916 (tt) outliers start: 10 outliers final: 6 residues processed: 65 average time/residue: 0.1048 time to fit residues: 8.8147 Evaluate side-chains 60 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 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: 8.9990 chunk 14 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 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 = 0.4220 r_free = 0.4220 target = 0.160653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.133446 restraints weight = 14053.502| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 8.47 r_work: 0.3498 rms_B_bonded: 8.30 restraints_weight: 2.0000 r_work: 0.3663 rms_B_bonded: 5.10 restraints_weight: 4.0000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3700 r_free = 0.3700 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3700 r_free = 0.3700 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2189 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= 0.225 Angle : 0.653 9.779 3996 Z= 0.332 Chirality : 0.041 0.220 480 Planarity : 0.004 0.044 496 Dihedral : 5.241 55.992 399 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.50 % Favored : 96.23 % Rotamer: Outliers : 3.52 % Allowed : 15.14 % 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: 2.39 (0.45), residues: 374 helix: 1.92 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.39 (0.96), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 364 HIS 0.001 0.000 HIS A 326 PHE 0.031 0.002 PHE A 180 TYR 0.017 0.002 TYR A 384 ARG 0.002 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 66 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.7624 (t80) REVERT: A 135 ILE cc_start: 0.8266 (OUTLIER) cc_final: 0.7883 (mp) REVERT: A 219 ASN cc_start: 0.8630 (t0) cc_final: 0.8399 (m-40) REVERT: A 340 LEU cc_start: 0.8266 (tt) cc_final: 0.8021 (tp) REVERT: A 368 LEU cc_start: 0.8155 (tp) cc_final: 0.7888 (tt) REVERT: A 395 PHE cc_start: 0.6007 (m-80) cc_final: 0.5643 (m-10) outliers start: 10 outliers final: 7 residues processed: 64 average time/residue: 0.0949 time to fit residues: 8.0473 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 : 0.281 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.158405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.124825 restraints weight = 15837.945| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 7.41 r_work (final): 0.3848 ------------------------------------------------------------------------------- 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: 0.7666 moved from start: 0.2381 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= 0.220 Angle : 0.647 9.330 3996 Z= 0.327 Chirality : 0.040 0.185 480 Planarity : 0.004 0.042 496 Dihedral : 5.118 52.180 399 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.23 % Favored : 96.50 % Rotamer: Outliers : 3.52 % Allowed : 16.20 % Favored : 80.28 % 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: 2.49 (0.45), residues: 374 helix: 1.98 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.32 (0.96), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 364 HIS 0.001 0.000 HIS A 326 PHE 0.037 0.001 PHE A 180 TYR 0.015 0.001 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 67 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.7506 (t80) REVERT: A 135 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.8098 (mp) REVERT: A 219 ASN cc_start: 0.8114 (t0) cc_final: 0.7912 (m-40) REVERT: A 368 LEU cc_start: 0.8313 (tp) cc_final: 0.8023 (tt) outliers start: 10 outliers final: 8 residues processed: 64 average time/residue: 0.1030 time to fit residues: 8.7549 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 : 0.276 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 16 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 4 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4183 r_free = 0.4183 target = 0.159218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.124906 restraints weight = 21450.848| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 9.03 r_work: 0.3516 rms_B_bonded: 8.72 restraints_weight: 2.0000 r_work: 0.3685 rms_B_bonded: 5.35 restraints_weight: 4.0000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 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= 0.218 Angle : 0.648 9.454 3996 Z= 0.328 Chirality : 0.041 0.232 480 Planarity : 0.004 0.040 496 Dihedral : 5.086 50.525 399 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.50 % Favored : 96.23 % Rotamer: Outliers : 3.17 % Allowed : 17.61 % Favored : 79.23 % 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 (0.45), residues: 374 helix: 2.00 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.44 (0.94), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 364 HIS 0.001 0.000 HIS A 326 PHE 0.035 0.002 PHE A 180 TYR 0.017 0.002 TYR A 384 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 64 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.8592 (OUTLIER) cc_final: 0.7736 (t80) REVERT: A 135 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8224 (mp) REVERT: A 219 ASN cc_start: 0.8584 (t0) cc_final: 0.8365 (m-40) REVERT: A 368 LEU cc_start: 0.8175 (tp) cc_final: 0.7912 (tt) REVERT: A 395 PHE cc_start: 0.6180 (m-80) cc_final: 0.5846 (m-10) outliers start: 9 outliers final: 7 residues processed: 61 average time/residue: 0.1014 time to fit residues: 8.1139 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 : 0.278 ------------------------------------------------------------------------------- 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 193 MET 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: 0.9980 chunk 22 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4231 r_free = 0.4231 target = 0.162190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.135901 restraints weight = 10718.928| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 6.40 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3951 r_free = 0.3951 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3951 r_free = 0.3951 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2590 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= 0.201 Angle : 0.635 9.360 3996 Z= 0.320 Chirality : 0.040 0.223 480 Planarity : 0.004 0.039 496 Dihedral : 4.986 48.287 399 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.23 % Favored : 96.50 % 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: 2.62 (0.45), residues: 374 helix: 2.13 (0.30), residues: 320 sheet: None (None), residues: 0 loop : -0.71 (0.88), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 364 HIS 0.001 0.000 HIS A 326 PHE 0.036 0.001 PHE A 180 TYR 0.015 0.002 TYR A 103 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 65 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.7740 (t80) REVERT: A 135 ILE cc_start: 0.8447 (OUTLIER) cc_final: 0.8214 (mp) REVERT: A 219 ASN cc_start: 0.8096 (t0) cc_final: 0.7890 (m-40) REVERT: A 289 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7430 (mp0) REVERT: A 368 LEU cc_start: 0.8344 (tp) cc_final: 0.8052 (tt) REVERT: A 395 PHE cc_start: 0.6278 (m-80) cc_final: 0.5820 (m-10) outliers start: 10 outliers final: 8 residues processed: 62 average time/residue: 0.1131 time to fit residues: 8.9502 Evaluate side-chains 61 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 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 14 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 5 optimal weight: 0.0370 chunk 24 optimal weight: 1.9990 overall best weight: 0.5660 ------------------------------------------------------------------------------- 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 = 0.4220 r_free = 0.4220 target = 0.161540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.133891 restraints weight = 15015.177| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 9.37 r_work: 0.3513 rms_B_bonded: 8.84 restraints_weight: 2.0000 r_work: 0.3683 rms_B_bonded: 5.41 restraints_weight: 4.0000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3724 r_free = 0.3724 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3724 r_free = 0.3724 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 2925 Z= 0.213 Angle : 0.643 9.303 3996 Z= 0.327 Chirality : 0.041 0.251 480 Planarity : 0.004 0.039 496 Dihedral : 4.975 47.208 399 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.23 % Favored : 96.50 % Rotamer: Outliers : 3.52 % Allowed : 17.25 % Favored : 79.23 % 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: 322 sheet: None (None), residues: 0 loop : -0.64 (0.88), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 364 HIS 0.001 0.000 HIS A 75 PHE 0.037 0.002 PHE A 180 TYR 0.015 0.001 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 62 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.351 Fit side-chains REVERT: A 13 GLU cc_start: 0.9067 (tp30) cc_final: 0.8289 (tp30) REVERT: A 133 PHE cc_start: 0.8473 (OUTLIER) cc_final: 0.7690 (t80) REVERT: A 135 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8175 (mp) REVERT: A 219 ASN cc_start: 0.8597 (t0) cc_final: 0.8368 (m-40) REVERT: A 226 GLU cc_start: 0.6360 (OUTLIER) cc_final: 0.6102 (mp0) REVERT: A 289 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7694 (mp0) REVERT: A 368 LEU cc_start: 0.8115 (tp) cc_final: 0.7844 (tt) REVERT: A 395 PHE cc_start: 0.6160 (m-80) cc_final: 0.5757 (m-10) outliers start: 10 outliers final: 7 residues processed: 59 average time/residue: 0.1116 time to fit residues: 8.4942 Evaluate side-chains 60 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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 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 23 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 6 optimal weight: 0.0970 chunk 21 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 = 0.163904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.131073 restraints weight = 15897.494| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 7.10 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3841 r_free = 0.3841 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 = 0.3841 r_free = 0.3841 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 2925 Z= 0.220 Angle : 0.650 9.354 3996 Z= 0.330 Chirality : 0.041 0.239 480 Planarity : 0.004 0.039 496 Dihedral : 4.948 46.342 399 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.23 % Favored : 96.50 % Rotamer: Outliers : 3.52 % Allowed : 17.61 % 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: 2.60 (0.45), residues: 374 helix: 2.10 (0.30), residues: 322 sheet: None (None), residues: 0 loop : -0.68 (0.88), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 364 HIS 0.001 0.000 HIS A 75 PHE 0.039 0.001 PHE A 180 TYR 0.018 0.002 TYR A 103 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 61 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.270 Fit side-chains REVERT: A 133 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.7656 (t80) REVERT: A 135 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8313 (mp) REVERT: A 226 GLU cc_start: 0.6511 (OUTLIER) cc_final: 0.6248 (mp0) REVERT: A 289 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7494 (mp0) REVERT: A 368 LEU cc_start: 0.8272 (tp) cc_final: 0.7975 (tt) outliers start: 10 outliers final: 7 residues processed: 58 average time/residue: 0.1010 time to fit residues: 7.7186 Evaluate side-chains 61 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 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 27 optimal weight: 0.3980 chunk 0 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 chunk 5 optimal weight: 0.0770 chunk 23 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 0.0970 chunk 4 optimal weight: 2.9990 overall best weight: 0.4136 ------------------------------------------------------------------------------- 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 = 0.4224 r_free = 0.4224 target = 0.162573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.134913 restraints weight = 12281.069| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 8.04 r_work: 0.3571 rms_B_bonded: 7.74 restraints_weight: 2.0000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3592 r_free = 0.3592 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 = 0.3592 r_free = 0.3592 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 2925 Z= 0.201 Angle : 0.636 9.310 3996 Z= 0.325 Chirality : 0.041 0.228 480 Planarity : 0.004 0.037 496 Dihedral : 4.957 44.722 399 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.50 % Favored : 96.23 % Rotamer: Outliers : 3.52 % Allowed : 17.61 % 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: 2.65 (0.45), residues: 374 helix: 2.14 (0.30), residues: 322 sheet: None (None), residues: 0 loop : -0.73 (0.88), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 364 HIS 0.001 0.000 HIS A 75 PHE 0.038 0.002 PHE A 180 TYR 0.014 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: 2189.87 seconds wall clock time: 38 minutes 1.00 seconds (2281.00 seconds total)