Starting phenix.real_space_refine on Sat May 10 04:42:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byi_45034/05_2025/9byi_45034_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byi_45034/05_2025/9byi_45034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9byi_45034/05_2025/9byi_45034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byi_45034/05_2025/9byi_45034.map" model { file = "/net/cci-nas-00/data/ceres_data/9byi_45034/05_2025/9byi_45034_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byi_45034/05_2025/9byi_45034_trim.cif" } resolution = 2.95 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= 0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 3 8.98 5 S 28 5.16 5 C 3042 2.51 5 N 708 2.21 5 O 724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 4505 Number of models: 1 Model: "" Number of chains: 4 Chain: "U" Number of atoms: 2107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2107 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 4, 'TRANS': 257} Chain breaks: 1 Chain: "A" Number of atoms: 2107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2107 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 4, 'TRANS': 257} Chain breaks: 1 Chain: "U" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 144 Unusual residues: {'D12': 4, 'EIC': 1, 'HEX': 2, 'OCT': 6, 'R16': 1} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "A" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 147 Unusual residues: {' K': 3, 'D12': 4, 'EIC': 1, 'HEX': 2, 'OCT': 6, 'R16': 1} Classifications: {'undetermined': 17} Link IDs: {None: 16} Time building chain proxies: 3.43, per 1000 atoms: 0.76 Number of scatterers: 4505 At special positions: 0 Unit cell: (64.5, 77.4, 98.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 3 19.00 S 28 16.00 O 724 8.00 N 708 7.00 C 3042 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.43 Conformation dependent library (CDL) restraints added in 499.4 milliseconds 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 77.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'U' and resid 14 through 64 removed outlier: 3.674A pdb=" N ALA U 40 " --> pdb=" O ALA U 36 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ALA U 44 " --> pdb=" O ALA U 40 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N HIS U 45 " --> pdb=" O LEU U 41 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS U 64 " --> pdb=" O PHE U 60 " (cutoff:3.500A) Processing helix chain 'U' and resid 68 through 85 Processing helix chain 'U' and resid 96 through 109 removed outlier: 3.626A pdb=" N SER U 109 " --> pdb=" O GLY U 105 " (cutoff:3.500A) Processing helix chain 'U' and resid 124 through 166 removed outlier: 4.424A pdb=" N SER U 136 " --> pdb=" O LEU U 132 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER U 137 " --> pdb=" O VAL U 133 " (cutoff:3.500A) Processing helix chain 'U' and resid 193 through 215 removed outlier: 3.827A pdb=" N MET U 215 " --> pdb=" O CYS U 211 " (cutoff:3.500A) Processing helix chain 'U' and resid 223 through 236 Processing helix chain 'U' and resid 255 through 295 removed outlier: 3.838A pdb=" N PHE U 259 " --> pdb=" O GLY U 255 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP U 295 " --> pdb=" O LEU U 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 64 removed outlier: 5.849A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N HIS A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 84 Processing helix chain 'A' and resid 97 through 109 removed outlier: 3.575A pdb=" N SER A 109 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 166 removed outlier: 4.422A pdb=" N SER A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 215 removed outlier: 3.669A pdb=" N MET A 215 " --> pdb=" O CYS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 236 Processing helix chain 'A' and resid 255 through 294 removed outlier: 3.894A pdb=" N PHE A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) 331 hydrogen bonds defined for protein. 993 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: 1.05 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 635 1.32 - 1.44: 1325 1.44 - 1.56: 2578 1.56 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 4578 Sorted by residual: bond pdb=" C TYR U 102 " pdb=" O TYR U 102 " ideal model delta sigma weight residual 1.236 1.193 0.044 1.26e-02 6.30e+03 1.20e+01 bond pdb=" C2 HEX U 401 " pdb=" C3 HEX U 401 " ideal model delta sigma weight residual 1.524 1.460 0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C2 HEX A 411 " pdb=" C3 HEX A 411 " ideal model delta sigma weight residual 1.524 1.462 0.062 2.00e-02 2.50e+03 9.63e+00 bond pdb=" N VAL A 91 " pdb=" CA VAL A 91 " ideal model delta sigma weight residual 1.455 1.496 -0.040 1.38e-02 5.25e+03 8.61e+00 bond pdb=" N ASP U 96 " pdb=" CA ASP U 96 " ideal model delta sigma weight residual 1.452 1.487 -0.034 1.22e-02 6.72e+03 7.82e+00 ... (remaining 4573 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 5999 2.47 - 4.93: 64 4.93 - 7.40: 6 7.40 - 9.86: 0 9.86 - 12.33: 3 Bond angle restraints: 6072 Sorted by residual: angle pdb=" N ASN A 90 " pdb=" CA ASN A 90 " pdb=" C ASN A 90 " ideal model delta sigma weight residual 111.24 123.57 -12.33 1.38e+00 5.25e-01 7.98e+01 angle pdb=" C ASN A 90 " pdb=" CA ASN A 90 " pdb=" CB ASN A 90 " ideal model delta sigma weight residual 112.09 106.00 6.09 1.54e+00 4.22e-01 1.57e+01 angle pdb=" N GLN A 164 " pdb=" CA GLN A 164 " pdb=" C GLN A 164 " ideal model delta sigma weight residual 111.36 107.21 4.15 1.09e+00 8.42e-01 1.45e+01 angle pdb=" CA TYR U 102 " pdb=" CB TYR U 102 " pdb=" CG TYR U 102 " ideal model delta sigma weight residual 113.90 120.21 -6.31 1.80e+00 3.09e-01 1.23e+01 angle pdb=" C3 HEX U 401 " pdb=" C4 HEX U 401 " pdb=" C5 HEX U 401 " ideal model delta sigma weight residual 113.35 123.56 -10.21 3.00e+00 1.11e-01 1.16e+01 ... (remaining 6067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.27: 2325 16.27 - 32.54: 239 32.54 - 48.81: 89 48.81 - 65.08: 28 65.08 - 81.35: 3 Dihedral angle restraints: 2684 sinusoidal: 1166 harmonic: 1518 Sorted by residual: dihedral pdb=" CA ASP A 96 " pdb=" C ASP A 96 " pdb=" N PHE A 97 " pdb=" CA PHE A 97 " ideal model delta harmonic sigma weight residual 180.00 155.68 24.32 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CB GLU U 252 " pdb=" CG GLU U 252 " pdb=" CD GLU U 252 " pdb=" OE1 GLU U 252 " ideal model delta sinusoidal sigma weight residual 0.00 -81.35 81.35 1 3.00e+01 1.11e-03 9.06e+00 dihedral pdb=" N ASN A 90 " pdb=" C ASN A 90 " pdb=" CA ASN A 90 " pdb=" CB ASN A 90 " ideal model delta harmonic sigma weight residual 122.80 130.29 -7.49 0 2.50e+00 1.60e-01 8.98e+00 ... (remaining 2681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 617 0.073 - 0.146: 27 0.146 - 0.219: 1 0.219 - 0.292: 0 0.292 - 0.365: 1 Chirality restraints: 646 Sorted by residual: chirality pdb=" CA ASN A 90 " pdb=" N ASN A 90 " pdb=" C ASN A 90 " pdb=" CB ASN A 90 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CA GLN A 164 " pdb=" N GLN A 164 " pdb=" C GLN A 164 " pdb=" CB GLN A 164 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA GLN A 285 " pdb=" N GLN A 285 " pdb=" C GLN A 285 " pdb=" CB GLN A 285 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.14e-01 ... (remaining 643 not shown) Planarity restraints: 730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 88 " 0.025 2.00e-02 2.50e+03 5.03e-02 2.53e+01 pdb=" C VAL A 88 " -0.087 2.00e-02 2.50e+03 pdb=" O VAL A 88 " 0.033 2.00e-02 2.50e+03 pdb=" N ASP A 89 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG U 94 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.75e+00 pdb=" C ARG U 94 " 0.045 2.00e-02 2.50e+03 pdb=" O ARG U 94 " -0.017 2.00e-02 2.50e+03 pdb=" N TRP U 95 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 217 " 0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO A 218 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 218 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 218 " 0.017 5.00e-02 4.00e+02 ... (remaining 727 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.85: 1510 2.85 - 3.42: 4800 3.42 - 4.00: 7333 4.00 - 4.57: 10656 4.57 - 5.14: 15507 Nonbonded interactions: 39806 Sorted by model distance: nonbonded pdb=" OH TYR U 78 " pdb=" OE2 GLU A 79 " model vdw 2.279 3.040 nonbonded pdb=" OE2 GLU U 220 " pdb=" OH TYR U 251 " model vdw 2.290 3.040 nonbonded pdb=" O SER A 236 " pdb=" OG1 THR A 237 " model vdw 2.319 3.040 nonbonded pdb=" O SER U 236 " pdb=" OG1 THR U 237 " model vdw 2.322 3.040 nonbonded pdb=" O SER A 109 " pdb=" OG1 THR A 110 " model vdw 2.349 3.040 ... (remaining 39801 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 295 or resid 406 through 408 or resid 410 or re \ sid 412 through 414)) selection = (chain 'U' and (resid 14 through 295 or resid 406 through 408 or resid 410 or re \ sid 412 through 414)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.710 Find NCS groups from input model: 0.190 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:14.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 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 : 0.005 0.064 4578 Z= 0.255 Angle : 0.654 12.327 6072 Z= 0.363 Chirality : 0.036 0.365 646 Planarity : 0.003 0.050 730 Dihedral : 15.740 81.350 1712 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 11.04 % Favored : 88.96 % 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: 4.10 (0.39), residues: 516 helix: 3.76 (0.25), residues: 416 sheet: None (None), residues: 0 loop : -2.40 (0.57), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 53 HIS 0.002 0.001 HIS A 250 PHE 0.010 0.001 PHE A 20 TYR 0.010 0.002 TYR A 30 ARG 0.005 0.000 ARG U 83 Details of bonding type rmsd hydrogen bonds : bond 0.11781 ( 331) hydrogen bonds : angle 3.60464 ( 993) covalent geometry : bond 0.00454 ( 4578) covalent geometry : angle 0.65422 ( 6072) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.489 Fit side-chains REVERT: U 191 LYS cc_start: 0.9342 (mttt) cc_final: 0.9104 (pttt) REVERT: A 191 LYS cc_start: 0.9224 (mmtt) cc_final: 0.8996 (tttt) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 1.5281 time to fit residues: 156.0059 Evaluate side-chains 56 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 0.0010 chunk 13 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 247 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.090320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.071469 restraints weight = 10097.804| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 3.10 r_work: 0.2779 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4578 Z= 0.151 Angle : 0.567 7.229 6072 Z= 0.306 Chirality : 0.033 0.132 646 Planarity : 0.003 0.031 730 Dihedral : 13.339 59.534 780 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.15 % Allowed : 15.09 % Favored : 81.76 % 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: 4.52 (0.39), residues: 516 helix: 4.19 (0.25), residues: 410 sheet: None (None), residues: 0 loop : -2.52 (0.57), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 95 HIS 0.003 0.001 HIS A 64 PHE 0.010 0.001 PHE U 262 TYR 0.020 0.001 TYR U 155 ARG 0.007 0.000 ARG U 62 Details of bonding type rmsd hydrogen bonds : bond 0.07068 ( 331) hydrogen bonds : angle 3.01241 ( 993) covalent geometry : bond 0.00308 ( 4578) covalent geometry : angle 0.56745 ( 6072) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.521 Fit side-chains REVERT: U 191 LYS cc_start: 0.9512 (mttt) cc_final: 0.9037 (pttt) REVERT: A 46 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8431 (tt0) REVERT: A 191 LYS cc_start: 0.9448 (mmtt) cc_final: 0.8912 (tttt) REVERT: A 293 LYS cc_start: 0.8884 (tppp) cc_final: 0.8652 (tppt) outliers start: 14 outliers final: 5 residues processed: 78 average time/residue: 1.1497 time to fit residues: 93.3241 Evaluate side-chains 64 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 156 ILE Chi-restraints excluded: chain U residue 207 LEU Chi-restraints excluded: chain U residue 273 TYR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 247 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 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 = 0.3286 r_free = 0.3286 target = 0.090868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.072206 restraints weight = 10055.631| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.05 r_work: 0.2802 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4578 Z= 0.135 Angle : 0.518 6.362 6072 Z= 0.280 Chirality : 0.033 0.155 646 Planarity : 0.002 0.022 730 Dihedral : 11.067 59.647 780 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.38 % Allowed : 15.32 % Favored : 81.31 % 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: 4.74 (0.39), residues: 516 helix: 4.39 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -2.53 (0.57), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 95 HIS 0.002 0.001 HIS A 64 PHE 0.008 0.001 PHE A 262 TYR 0.008 0.001 TYR A 30 ARG 0.003 0.000 ARG U 62 Details of bonding type rmsd hydrogen bonds : bond 0.06526 ( 331) hydrogen bonds : angle 2.87497 ( 993) covalent geometry : bond 0.00264 ( 4578) covalent geometry : angle 0.51847 ( 6072) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 46 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8501 (tt0) REVERT: U 191 LYS cc_start: 0.9502 (mttt) cc_final: 0.9045 (pttt) REVERT: A 46 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8489 (tt0) REVERT: A 191 LYS cc_start: 0.9471 (mmtt) cc_final: 0.8947 (tttt) outliers start: 15 outliers final: 9 residues processed: 79 average time/residue: 0.9917 time to fit residues: 81.8970 Evaluate side-chains 69 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 46 GLU Chi-restraints excluded: chain U residue 156 ILE Chi-restraints excluded: chain U residue 207 LEU Chi-restraints excluded: chain U residue 256 LEU Chi-restraints excluded: chain U residue 273 TYR Chi-restraints excluded: chain U residue 280 SER Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 247 GLN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 286 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 8 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3249 r_free = 0.3249 target = 0.088170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.069606 restraints weight = 10066.145| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 3.04 r_work: 0.2746 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4578 Z= 0.159 Angle : 0.555 7.383 6072 Z= 0.297 Chirality : 0.033 0.147 646 Planarity : 0.002 0.023 730 Dihedral : 9.941 59.125 780 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 1.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.70 % Allowed : 17.57 % Favored : 79.73 % 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: 4.79 (0.40), residues: 516 helix: 4.44 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -2.56 (0.58), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 95 HIS 0.002 0.000 HIS A 64 PHE 0.010 0.001 PHE U 262 TYR 0.021 0.001 TYR U 155 ARG 0.002 0.000 ARG U 62 Details of bonding type rmsd hydrogen bonds : bond 0.07323 ( 331) hydrogen bonds : angle 3.05920 ( 993) covalent geometry : bond 0.00336 ( 4578) covalent geometry : angle 0.55488 ( 6072) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: U 158 LYS cc_start: 0.9067 (tmmt) cc_final: 0.8560 (tppp) REVERT: U 191 LYS cc_start: 0.9533 (mttt) cc_final: 0.9045 (pttt) REVERT: A 46 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8522 (tt0) REVERT: A 191 LYS cc_start: 0.9515 (mmtt) cc_final: 0.8912 (tttt) outliers start: 12 outliers final: 9 residues processed: 66 average time/residue: 1.1769 time to fit residues: 81.0122 Evaluate side-chains 68 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 156 ILE Chi-restraints excluded: chain U residue 207 LEU Chi-restraints excluded: chain U residue 256 LEU Chi-restraints excluded: chain U residue 280 SER Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 247 GLN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 286 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 27 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 0 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 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 = 0.3309 r_free = 0.3309 target = 0.091941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.073087 restraints weight = 10313.496| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 3.11 r_work: 0.2813 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4578 Z= 0.135 Angle : 0.531 6.910 6072 Z= 0.281 Chirality : 0.032 0.116 646 Planarity : 0.002 0.022 730 Dihedral : 8.646 59.224 780 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.93 % Allowed : 16.44 % Favored : 80.63 % 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: 4.93 (0.40), residues: 516 helix: 4.52 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -2.46 (0.59), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 95 HIS 0.004 0.001 HIS A 64 PHE 0.008 0.001 PHE U 262 TYR 0.016 0.001 TYR U 155 ARG 0.001 0.000 ARG A 68 Details of bonding type rmsd hydrogen bonds : bond 0.06270 ( 331) hydrogen bonds : angle 2.78927 ( 993) covalent geometry : bond 0.00275 ( 4578) covalent geometry : angle 0.53069 ( 6072) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: U 46 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8504 (tt0) REVERT: U 158 LYS cc_start: 0.9028 (tmmt) cc_final: 0.8552 (tppp) REVERT: U 191 LYS cc_start: 0.9530 (mttt) cc_final: 0.9055 (pttt) REVERT: U 213 SER cc_start: 0.8834 (m) cc_final: 0.8182 (t) REVERT: A 46 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8479 (tt0) REVERT: A 191 LYS cc_start: 0.9535 (mmtt) cc_final: 0.8909 (tttt) REVERT: A 293 LYS cc_start: 0.8806 (tppt) cc_final: 0.8289 (tppp) outliers start: 13 outliers final: 9 residues processed: 74 average time/residue: 1.1991 time to fit residues: 92.3760 Evaluate side-chains 66 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 46 GLU Chi-restraints excluded: chain U residue 156 ILE Chi-restraints excluded: chain U residue 207 LEU Chi-restraints excluded: chain U residue 256 LEU Chi-restraints excluded: chain U residue 273 TYR Chi-restraints excluded: chain U residue 280 SER Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 247 GLN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 286 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 33 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.3223 r_free = 0.3223 target = 0.086076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.067263 restraints weight = 10089.470| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 3.07 r_work: 0.2695 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4578 Z= 0.186 Angle : 0.585 6.199 6072 Z= 0.314 Chirality : 0.033 0.113 646 Planarity : 0.002 0.021 730 Dihedral : 8.944 58.862 780 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 2.70 % Allowed : 17.79 % Favored : 79.50 % 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: 4.76 (0.40), residues: 516 helix: 4.47 (0.24), residues: 406 sheet: None (None), residues: 0 loop : -2.67 (0.59), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 95 HIS 0.004 0.001 HIS A 64 PHE 0.010 0.001 PHE U 262 TYR 0.009 0.001 TYR A 216 ARG 0.001 0.000 ARG U 19 Details of bonding type rmsd hydrogen bonds : bond 0.07962 ( 331) hydrogen bonds : angle 3.23480 ( 993) covalent geometry : bond 0.00414 ( 4578) covalent geometry : angle 0.58473 ( 6072) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: U 46 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8516 (tt0) REVERT: U 158 LYS cc_start: 0.9059 (tmmt) cc_final: 0.8573 (tppp) REVERT: U 191 LYS cc_start: 0.9541 (mttt) cc_final: 0.9045 (pttt) REVERT: A 46 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8482 (tt0) REVERT: A 90 ASN cc_start: 0.8910 (m110) cc_final: 0.8568 (p0) REVERT: A 191 LYS cc_start: 0.9544 (mmtt) cc_final: 0.8873 (tttt) outliers start: 12 outliers final: 8 residues processed: 67 average time/residue: 1.1405 time to fit residues: 79.6347 Evaluate side-chains 66 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 46 GLU Chi-restraints excluded: chain U residue 156 ILE Chi-restraints excluded: chain U residue 207 LEU Chi-restraints excluded: chain U residue 211 CYS Chi-restraints excluded: chain U residue 256 LEU Chi-restraints excluded: chain U residue 280 SER Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 247 GLN Chi-restraints excluded: chain A residue 280 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 18 optimal weight: 0.0670 chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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 = 0.3302 r_free = 0.3302 target = 0.091597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.072446 restraints weight = 10091.440| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.11 r_work: 0.2794 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4578 Z= 0.141 Angle : 0.561 7.006 6072 Z= 0.297 Chirality : 0.032 0.102 646 Planarity : 0.002 0.024 730 Dihedral : 8.017 59.802 780 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.70 % Allowed : 18.24 % Favored : 79.05 % 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: 5.01 (0.40), residues: 516 helix: 4.56 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -2.36 (0.61), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 95 HIS 0.003 0.000 HIS A 64 PHE 0.007 0.001 PHE U 262 TYR 0.007 0.001 TYR A 30 ARG 0.001 0.000 ARG A 68 Details of bonding type rmsd hydrogen bonds : bond 0.06385 ( 331) hydrogen bonds : angle 2.81371 ( 993) covalent geometry : bond 0.00291 ( 4578) covalent geometry : angle 0.56136 ( 6072) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.464 Fit side-chains REVERT: U 46 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8502 (tt0) REVERT: U 158 LYS cc_start: 0.9007 (tmmt) cc_final: 0.8398 (tppp) REVERT: U 190 TRP cc_start: 0.8708 (m100) cc_final: 0.7866 (m-10) REVERT: U 191 LYS cc_start: 0.9529 (mttt) cc_final: 0.9061 (pttt) REVERT: A 46 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8465 (tt0) REVERT: A 90 ASN cc_start: 0.8902 (m110) cc_final: 0.8590 (p0) REVERT: A 191 LYS cc_start: 0.9545 (mmtt) cc_final: 0.8871 (tttt) outliers start: 12 outliers final: 8 residues processed: 66 average time/residue: 0.9959 time to fit residues: 68.7919 Evaluate side-chains 66 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 46 GLU Chi-restraints excluded: chain U residue 156 ILE Chi-restraints excluded: chain U residue 207 LEU Chi-restraints excluded: chain U residue 256 LEU Chi-restraints excluded: chain U residue 280 SER Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 247 GLN Chi-restraints excluded: chain A residue 280 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 6 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3276 r_free = 0.3276 target = 0.090375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.071080 restraints weight = 10043.826| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 3.13 r_work: 0.2766 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4578 Z= 0.151 Angle : 0.590 7.952 6072 Z= 0.313 Chirality : 0.032 0.103 646 Planarity : 0.002 0.020 730 Dihedral : 7.956 59.177 780 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.25 % Allowed : 18.69 % Favored : 79.05 % 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: 4.94 (0.40), residues: 516 helix: 4.51 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -2.39 (0.61), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 95 HIS 0.003 0.001 HIS A 64 PHE 0.009 0.001 PHE U 262 TYR 0.006 0.001 TYR U 30 ARG 0.001 0.000 ARG A 292 Details of bonding type rmsd hydrogen bonds : bond 0.06680 ( 331) hydrogen bonds : angle 2.90010 ( 993) covalent geometry : bond 0.00327 ( 4578) covalent geometry : angle 0.59009 ( 6072) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.471 Fit side-chains REVERT: U 46 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8502 (tt0) REVERT: U 158 LYS cc_start: 0.9014 (tmmt) cc_final: 0.8422 (tppp) REVERT: U 190 TRP cc_start: 0.8726 (m100) cc_final: 0.7845 (m-10) REVERT: U 191 LYS cc_start: 0.9523 (mttt) cc_final: 0.9044 (pttt) REVERT: A 46 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8458 (tt0) REVERT: A 90 ASN cc_start: 0.8899 (m110) cc_final: 0.8593 (p0) REVERT: A 191 LYS cc_start: 0.9550 (mmtt) cc_final: 0.8864 (tttt) REVERT: A 293 LYS cc_start: 0.8701 (tppt) cc_final: 0.8191 (tppp) outliers start: 10 outliers final: 8 residues processed: 63 average time/residue: 1.0634 time to fit residues: 70.0306 Evaluate side-chains 65 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 46 GLU Chi-restraints excluded: chain U residue 156 ILE Chi-restraints excluded: chain U residue 207 LEU Chi-restraints excluded: chain U residue 256 LEU Chi-restraints excluded: chain U residue 280 SER Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 247 GLN Chi-restraints excluded: chain A residue 280 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 21 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 47 optimal weight: 0.0570 chunk 36 optimal weight: 0.0000 chunk 29 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.4102 ------------------------------------------------------------------------------- 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 = 0.3364 r_free = 0.3364 target = 0.095409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.076577 restraints weight = 10052.413| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.09 r_work: 0.2886 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4578 Z= 0.133 Angle : 0.578 7.870 6072 Z= 0.303 Chirality : 0.031 0.102 646 Planarity : 0.002 0.023 730 Dihedral : 7.134 58.179 780 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.80 % Allowed : 19.14 % Favored : 79.05 % 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: 5.05 (0.40), residues: 516 helix: 4.56 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -2.21 (0.62), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 95 HIS 0.002 0.000 HIS A 64 PHE 0.006 0.001 PHE A 232 TYR 0.006 0.001 TYR A 30 ARG 0.001 0.000 ARG A 292 Details of bonding type rmsd hydrogen bonds : bond 0.05195 ( 331) hydrogen bonds : angle 2.59166 ( 993) covalent geometry : bond 0.00285 ( 4578) covalent geometry : angle 0.57815 ( 6072) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.390 Fit side-chains REVERT: U 46 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8515 (tt0) REVERT: U 158 LYS cc_start: 0.8955 (tmmt) cc_final: 0.8416 (tppp) REVERT: U 190 TRP cc_start: 0.8682 (m100) cc_final: 0.7839 (m-10) REVERT: U 191 LYS cc_start: 0.9520 (mttt) cc_final: 0.9080 (pttt) REVERT: U 213 SER cc_start: 0.8708 (m) cc_final: 0.8055 (t) REVERT: A 46 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8468 (tt0) REVERT: A 90 ASN cc_start: 0.8970 (m110) cc_final: 0.8671 (p0) REVERT: A 191 LYS cc_start: 0.9559 (mmtt) cc_final: 0.8890 (tttt) REVERT: A 213 SER cc_start: 0.8738 (m) cc_final: 0.8227 (t) outliers start: 8 outliers final: 4 residues processed: 71 average time/residue: 0.9322 time to fit residues: 69.3447 Evaluate side-chains 59 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 46 GLU Chi-restraints excluded: chain U residue 156 ILE Chi-restraints excluded: chain U residue 207 LEU Chi-restraints excluded: chain U residue 280 SER Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 280 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 5 optimal weight: 0.2980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.091621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.072740 restraints weight = 10097.017| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 3.06 r_work: 0.2808 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4578 Z= 0.145 Angle : 0.612 8.802 6072 Z= 0.321 Chirality : 0.032 0.100 646 Planarity : 0.002 0.019 730 Dihedral : 7.290 57.186 780 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 1.80 % Allowed : 19.59 % Favored : 78.60 % 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: 5.03 (0.40), residues: 516 helix: 4.55 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -2.21 (0.63), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 95 HIS 0.003 0.000 HIS A 64 PHE 0.009 0.001 PHE U 262 TYR 0.019 0.001 TYR U 155 ARG 0.001 0.000 ARG U 19 Details of bonding type rmsd hydrogen bonds : bond 0.06022 ( 331) hydrogen bonds : angle 2.74135 ( 993) covalent geometry : bond 0.00316 ( 4578) covalent geometry : angle 0.61211 ( 6072) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.417 Fit side-chains REVERT: U 46 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8527 (tt0) REVERT: U 158 LYS cc_start: 0.8993 (tmmt) cc_final: 0.8458 (tppp) REVERT: U 190 TRP cc_start: 0.8715 (m100) cc_final: 0.7807 (m-10) REVERT: U 191 LYS cc_start: 0.9515 (mttt) cc_final: 0.9061 (pttt) REVERT: A 46 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8468 (tt0) REVERT: A 90 ASN cc_start: 0.8984 (m110) cc_final: 0.8697 (p0) REVERT: A 191 LYS cc_start: 0.9572 (mmtt) cc_final: 0.8890 (tttt) outliers start: 8 outliers final: 6 residues processed: 61 average time/residue: 1.0494 time to fit residues: 67.0456 Evaluate side-chains 60 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 46 GLU Chi-restraints excluded: chain U residue 156 ILE Chi-restraints excluded: chain U residue 207 LEU Chi-restraints excluded: chain U residue 280 SER Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 286 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 0.2980 chunk 37 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3293 r_free = 0.3293 target = 0.091692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.072388 restraints weight = 9954.033| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.17 r_work: 0.2803 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4578 Z= 0.142 Angle : 0.603 8.799 6072 Z= 0.317 Chirality : 0.032 0.100 646 Planarity : 0.002 0.021 730 Dihedral : 7.207 57.149 780 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 1.80 % Allowed : 19.82 % Favored : 78.38 % 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: 5.03 (0.40), residues: 516 helix: 4.54 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -2.17 (0.63), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 95 HIS 0.003 0.000 HIS A 64 PHE 0.008 0.001 PHE U 262 TYR 0.021 0.001 TYR U 155 ARG 0.001 0.000 ARG U 19 Details of bonding type rmsd hydrogen bonds : bond 0.05943 ( 331) hydrogen bonds : angle 2.70864 ( 993) covalent geometry : bond 0.00308 ( 4578) covalent geometry : angle 0.60333 ( 6072) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2842.98 seconds wall clock time: 50 minutes 20.73 seconds (3020.73 seconds total)