Starting phenix.real_space_refine on Fri Aug 22 15:35:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byi_45034/08_2025/9byi_45034_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byi_45034/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9byi_45034/08_2025/9byi_45034_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byi_45034/08_2025/9byi_45034_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9byi_45034/08_2025/9byi_45034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byi_45034/08_2025/9byi_45034.map" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.26, per 1000 atoms: 0.28 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: 0.40 Conformation dependent library (CDL) restraints added in 142.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.11 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: 0.60 Time building geometry restraints manager: 0.44 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: 1.520 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: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.710 Find NCS groups from input model: 0.070 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: 0.000 Load rotamer database and sin/cos tables:6.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.660 ------------------------------------------------------------------------------- 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 : 3.00 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.000 ARG U 83 TYR 0.010 0.002 TYR A 30 PHE 0.010 0.001 PHE A 20 TRP 0.008 0.001 TRP U 53 HIS 0.002 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 4578) covalent geometry : angle 0.65422 ( 6072) hydrogen bonds : bond 0.11781 ( 331) hydrogen bonds : angle 3.60464 ( 993) *********************** 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 : 0.120 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: 0.6406 time to fit residues: 65.3006 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 : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3282 r_free = 0.3282 target = 0.090620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.071814 restraints weight = 10126.349| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 3.10 r_work: 0.2778 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4578 Z= 0.150 Angle : 0.560 7.131 6072 Z= 0.303 Chirality : 0.033 0.137 646 Planarity : 0.003 0.029 730 Dihedral : 13.481 59.596 780 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 1.07 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.000 ARG U 62 TYR 0.019 0.001 TYR U 155 PHE 0.010 0.001 PHE U 262 TRP 0.010 0.001 TRP A 95 HIS 0.003 0.001 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 4578) covalent geometry : angle 0.56042 ( 6072) hydrogen bonds : bond 0.07047 ( 331) hydrogen bonds : angle 3.00901 ( 993) *********************** 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 : 0.162 Fit side-chains REVERT: U 191 LYS cc_start: 0.9509 (mttt) cc_final: 0.9010 (pttt) REVERT: A 46 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8413 (tt0) REVERT: A 191 LYS cc_start: 0.9441 (mmtt) cc_final: 0.8906 (tttt) REVERT: A 293 LYS cc_start: 0.8868 (tppp) cc_final: 0.8629 (tppt) outliers start: 14 outliers final: 5 residues processed: 78 average time/residue: 0.4981 time to fit residues: 40.2799 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 : 0.122 ------------------------------------------------------------------------------- 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 31 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 33 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 49 optimal weight: 0.4980 chunk 2 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 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 = 0.3290 r_free = 0.3290 target = 0.090994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.072337 restraints weight = 10133.904| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.08 r_work: 0.2801 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4578 Z= 0.135 Angle : 0.520 6.495 6072 Z= 0.280 Chirality : 0.032 0.147 646 Planarity : 0.002 0.022 730 Dihedral : 11.021 59.919 780 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 1.07 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.73 (0.39), residues: 516 helix: 4.39 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -2.55 (0.57), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG U 62 TYR 0.008 0.001 TYR A 30 PHE 0.008 0.001 PHE A 262 TRP 0.010 0.001 TRP A 95 HIS 0.001 0.000 HIS U 64 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 4578) covalent geometry : angle 0.51995 ( 6072) hydrogen bonds : bond 0.06493 ( 331) hydrogen bonds : angle 2.86552 ( 993) *********************** 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 84 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.105 Fit side-chains revert: symmetry clash REVERT: U 46 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8483 (tt0) REVERT: U 158 LYS cc_start: 0.9047 (tmmt) cc_final: 0.8531 (tppp) REVERT: U 191 LYS cc_start: 0.9487 (mttt) cc_final: 0.9028 (pttt) REVERT: A 46 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8483 (tt0) REVERT: A 191 LYS cc_start: 0.9470 (mmtt) cc_final: 0.8949 (tttt) outliers start: 15 outliers final: 9 residues processed: 80 average time/residue: 0.4327 time to fit residues: 36.0091 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 : 0.100 ------------------------------------------------------------------------------- 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 30 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 0.0370 chunk 19 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.7460 ------------------------------------------------------------------------------- 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 = 0.3295 r_free = 0.3295 target = 0.091343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.072804 restraints weight = 10095.466| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.03 r_work: 0.2817 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 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 0.027 4578 Z= 0.134 Angle : 0.527 7.767 6072 Z= 0.280 Chirality : 0.032 0.147 646 Planarity : 0.002 0.022 730 Dihedral : 9.300 58.356 780 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.48 % Allowed : 17.34 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.87 (0.39), residues: 516 helix: 4.48 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -2.47 (0.58), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG U 62 TYR 0.021 0.001 TYR U 155 PHE 0.008 0.001 PHE U 262 TRP 0.009 0.001 TRP A 95 HIS 0.003 0.000 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 4578) covalent geometry : angle 0.52702 ( 6072) hydrogen bonds : bond 0.06292 ( 331) hydrogen bonds : angle 2.80316 ( 993) *********************** 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 76 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.115 Fit side-chains revert: symmetry clash REVERT: U 158 LYS cc_start: 0.9041 (tmmt) cc_final: 0.8545 (tppp) REVERT: U 191 LYS cc_start: 0.9506 (mttt) cc_final: 0.9056 (pttt) REVERT: A 46 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8466 (tt0) REVERT: A 191 LYS cc_start: 0.9493 (mmtt) cc_final: 0.8931 (tttt) outliers start: 11 outliers final: 9 residues processed: 71 average time/residue: 0.4268 time to fit residues: 31.5338 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 : 0.104 ------------------------------------------------------------------------------- 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 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 215 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.090839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.072118 restraints weight = 10155.215| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.05 r_work: 0.2799 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4578 Z= 0.138 Angle : 0.529 6.711 6072 Z= 0.281 Chirality : 0.032 0.119 646 Planarity : 0.002 0.021 730 Dihedral : 8.669 59.576 780 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.48 % Allowed : 17.79 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.93 (0.39), residues: 516 helix: 4.53 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -2.48 (0.58), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG U 52 TYR 0.009 0.001 TYR U 229 PHE 0.009 0.001 PHE U 262 TRP 0.009 0.001 TRP A 95 HIS 0.003 0.001 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 4578) covalent geometry : angle 0.52924 ( 6072) hydrogen bonds : bond 0.06448 ( 331) hydrogen bonds : angle 2.83487 ( 993) *********************** 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 72 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: U 46 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8522 (tt0) REVERT: U 158 LYS cc_start: 0.9046 (tmmt) cc_final: 0.8566 (tppp) REVERT: U 191 LYS cc_start: 0.9527 (mttt) cc_final: 0.9060 (pttt) REVERT: A 46 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8478 (tt0) REVERT: A 90 ASN cc_start: 0.8870 (m110) cc_final: 0.8394 (p0) REVERT: A 191 LYS cc_start: 0.9525 (mmtt) cc_final: 0.8919 (tttt) REVERT: A 293 LYS cc_start: 0.8834 (tppt) cc_final: 0.8328 (tppp) outliers start: 11 outliers final: 8 residues processed: 68 average time/residue: 0.4455 time to fit residues: 31.6486 Evaluate side-chains 64 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.116 ------------------------------------------------------------------------------- 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 215 MET 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 17 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 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 = 0.3294 r_free = 0.3294 target = 0.091177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.072253 restraints weight = 10346.030| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.08 r_work: 0.2804 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2567 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= 0.136 Angle : 0.528 6.321 6072 Z= 0.281 Chirality : 0.032 0.108 646 Planarity : 0.002 0.022 730 Dihedral : 8.232 59.709 780 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.48 % Allowed : 18.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.98 (0.40), residues: 516 helix: 4.55 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -2.38 (0.60), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG U 19 TYR 0.021 0.001 TYR U 155 PHE 0.008 0.001 PHE U 262 TRP 0.009 0.001 TRP A 95 HIS 0.003 0.001 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 4578) covalent geometry : angle 0.52811 ( 6072) hydrogen bonds : bond 0.06321 ( 331) hydrogen bonds : angle 2.79651 ( 993) *********************** 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: 11 poor density : 61 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 46 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8537 (tt0) REVERT: U 158 LYS cc_start: 0.9032 (tmmt) cc_final: 0.8566 (tppp) REVERT: U 191 LYS cc_start: 0.9516 (mttt) cc_final: 0.9068 (pttt) REVERT: A 46 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8505 (tt0) REVERT: A 90 ASN cc_start: 0.8891 (m110) cc_final: 0.8513 (p0) REVERT: A 191 LYS cc_start: 0.9539 (mmtt) cc_final: 0.8904 (tttt) outliers start: 11 outliers final: 9 residues processed: 68 average time/residue: 0.4350 time to fit residues: 30.7841 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 : 0.168 ------------------------------------------------------------------------------- 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 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 215 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 48 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 18 optimal weight: 0.1980 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 10 optimal weight: 0.0020 chunk 41 optimal weight: 0.0170 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.3426 ------------------------------------------------------------------------------- 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 = 0.3402 r_free = 0.3402 target = 0.098358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.079223 restraints weight = 10017.665| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.10 r_work: 0.2926 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 4578 Z= 0.121 Angle : 0.524 6.697 6072 Z= 0.275 Chirality : 0.031 0.103 646 Planarity : 0.002 0.020 730 Dihedral : 7.208 59.911 780 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.35 % Allowed : 19.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.09 (0.39), residues: 516 helix: 4.63 (0.24), residues: 406 sheet: None (None), residues: 0 loop : -2.22 (0.61), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 68 TYR 0.008 0.001 TYR U 229 PHE 0.006 0.001 PHE U 232 TRP 0.011 0.001 TRP A 95 HIS 0.003 0.000 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 4578) covalent geometry : angle 0.52367 ( 6072) hydrogen bonds : bond 0.04855 ( 331) hydrogen bonds : angle 2.49847 ( 993) *********************** 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 73 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.181 Fit side-chains REVERT: U 158 LYS cc_start: 0.8948 (tmmt) cc_final: 0.8705 (tppp) REVERT: U 162 GLN cc_start: 0.9388 (tm-30) cc_final: 0.8996 (pt0) REVERT: U 190 TRP cc_start: 0.8570 (m100) cc_final: 0.7858 (m-10) REVERT: U 191 LYS cc_start: 0.9516 (mttt) cc_final: 0.9087 (pttt) REVERT: U 213 SER cc_start: 0.8715 (m) cc_final: 0.8089 (t) REVERT: A 46 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8503 (tt0) REVERT: A 90 ASN cc_start: 0.8933 (m110) cc_final: 0.8469 (p0) REVERT: A 162 GLN cc_start: 0.9258 (tm-30) cc_final: 0.8877 (mt0) REVERT: A 191 LYS cc_start: 0.9527 (mmtt) cc_final: 0.8884 (tttt) outliers start: 6 outliers final: 4 residues processed: 71 average time/residue: 0.4113 time to fit residues: 30.6294 Evaluate side-chains 56 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.107 ------------------------------------------------------------------------------- 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 208 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3244 r_free = 0.3244 target = 0.088782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.069273 restraints weight = 10142.551| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 3.19 r_work: 0.2726 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4578 Z= 0.176 Angle : 0.596 7.246 6072 Z= 0.316 Chirality : 0.034 0.109 646 Planarity : 0.002 0.019 730 Dihedral : 8.163 59.471 780 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 1.58 % Allowed : 20.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.89 (0.40), residues: 516 helix: 4.52 (0.24), residues: 406 sheet: None (None), residues: 0 loop : -2.45 (0.61), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG U 62 TYR 0.020 0.001 TYR U 155 PHE 0.011 0.001 PHE U 262 TRP 0.011 0.001 TRP A 190 HIS 0.004 0.001 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 4578) covalent geometry : angle 0.59592 ( 6072) hydrogen bonds : bond 0.07474 ( 331) hydrogen bonds : angle 3.12567 ( 993) *********************** 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 64 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.168 Fit side-chains REVERT: U 158 LYS cc_start: 0.9064 (tmmt) cc_final: 0.8425 (tppp) REVERT: U 190 TRP cc_start: 0.8743 (m100) cc_final: 0.7926 (m-10) REVERT: U 191 LYS cc_start: 0.9518 (mttt) cc_final: 0.9042 (pttt) REVERT: A 46 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8480 (tt0) REVERT: A 90 ASN cc_start: 0.8900 (m110) cc_final: 0.8572 (p0) REVERT: A 157 MET cc_start: 0.9054 (ttm) cc_final: 0.8566 (tmm) REVERT: A 190 TRP cc_start: 0.8868 (m100) cc_final: 0.8468 (m-10) REVERT: A 191 LYS cc_start: 0.9507 (mmtt) cc_final: 0.8798 (ptmt) REVERT: A 293 LYS cc_start: 0.8827 (tppp) cc_final: 0.8532 (tppp) outliers start: 7 outliers final: 5 residues processed: 62 average time/residue: 0.4181 time to fit residues: 27.1165 Evaluate side-chains 61 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.120 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 chunk 36 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3282 r_free = 0.3282 target = 0.090259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.071516 restraints weight = 10176.088| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.04 r_work: 0.2787 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4578 Z= 0.147 Angle : 0.591 7.686 6072 Z= 0.311 Chirality : 0.032 0.100 646 Planarity : 0.002 0.023 730 Dihedral : 7.665 59.134 780 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.80 % Allowed : 20.50 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.99 (0.40), residues: 516 helix: 4.52 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -2.22 (0.62), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG U 19 TYR 0.020 0.001 TYR U 155 PHE 0.008 0.001 PHE U 262 TRP 0.008 0.001 TRP A 95 HIS 0.003 0.000 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 4578) covalent geometry : angle 0.59069 ( 6072) hydrogen bonds : bond 0.06471 ( 331) hydrogen bonds : angle 2.85000 ( 993) *********************** 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 64 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: U 158 LYS cc_start: 0.9036 (tmmt) cc_final: 0.8718 (tppp) REVERT: U 162 GLN cc_start: 0.9386 (tm-30) cc_final: 0.8989 (pt0) REVERT: U 190 TRP cc_start: 0.8782 (m100) cc_final: 0.7904 (m-10) REVERT: U 191 LYS cc_start: 0.9524 (mttt) cc_final: 0.9064 (pttt) REVERT: U 293 LYS cc_start: 0.8850 (tppp) cc_final: 0.8524 (tppp) REVERT: A 46 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8583 (tt0) REVERT: A 90 ASN cc_start: 0.8975 (m110) cc_final: 0.8656 (p0) REVERT: A 191 LYS cc_start: 0.9524 (mmtt) cc_final: 0.8852 (tttt) outliers start: 8 outliers final: 7 residues processed: 63 average time/residue: 0.4137 time to fit residues: 27.2618 Evaluate side-chains 63 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.184 ------------------------------------------------------------------------------- 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 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 32 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3258 r_free = 0.3258 target = 0.089123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.070204 restraints weight = 10137.605| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 3.11 r_work: 0.2744 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4578 Z= 0.161 Angle : 0.617 8.088 6072 Z= 0.324 Chirality : 0.033 0.101 646 Planarity : 0.002 0.020 730 Dihedral : 7.873 58.969 780 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.58 % Allowed : 20.72 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.90 (0.40), residues: 516 helix: 4.48 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -2.35 (0.61), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG U 19 TYR 0.020 0.001 TYR U 155 PHE 0.010 0.001 PHE U 262 TRP 0.006 0.001 TRP A 53 HIS 0.003 0.000 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 4578) covalent geometry : angle 0.61746 ( 6072) hydrogen bonds : bond 0.06987 ( 331) hydrogen bonds : angle 2.97395 ( 993) ********************** 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 65 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: U 158 LYS cc_start: 0.9034 (tmmt) cc_final: 0.8721 (tppp) REVERT: U 162 GLN cc_start: 0.9381 (tm-30) cc_final: 0.8968 (pt0) REVERT: U 190 TRP cc_start: 0.8793 (m100) cc_final: 0.7815 (m-10) REVERT: U 191 LYS cc_start: 0.9520 (mttt) cc_final: 0.9047 (pttt) REVERT: A 46 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8472 (tt0) REVERT: A 90 ASN cc_start: 0.8971 (m110) cc_final: 0.8673 (p0) REVERT: A 191 LYS cc_start: 0.9507 (mmtt) cc_final: 0.8832 (tttt) REVERT: A 293 LYS cc_start: 0.8803 (tppp) cc_final: 0.8471 (tppp) outliers start: 7 outliers final: 7 residues processed: 64 average time/residue: 0.4336 time to fit residues: 28.9881 Evaluate side-chains 66 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.145 ------------------------------------------------------------------------------- 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 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 9 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.090114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.070976 restraints weight = 10112.059| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 3.18 r_work: 0.2767 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2828 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= 0.150 Angle : 0.606 8.776 6072 Z= 0.318 Chirality : 0.032 0.099 646 Planarity : 0.002 0.022 730 Dihedral : 7.631 59.415 780 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 1.80 % Allowed : 20.50 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.95 (0.40), residues: 516 helix: 4.51 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -2.31 (0.61), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG U 19 TYR 0.020 0.001 TYR U 155 PHE 0.008 0.001 PHE U 262 TRP 0.007 0.001 TRP A 289 HIS 0.003 0.000 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 4578) covalent geometry : angle 0.60645 ( 6072) hydrogen bonds : bond 0.06471 ( 331) hydrogen bonds : angle 2.84460 ( 993) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1344.63 seconds wall clock time: 23 minutes 38.37 seconds (1418.37 seconds total)