Starting phenix.real_space_refine on Wed Jul 1 23:26:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fzq_50894/07_2026/9fzq_50894.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fzq_50894/07_2026/9fzq_50894.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fzq_50894/07_2026/9fzq_50894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fzq_50894/07_2026/9fzq_50894.map" model { file = "/net/cci-nas-00/data/ceres_data/9fzq_50894/07_2026/9fzq_50894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fzq_50894/07_2026/9fzq_50894.cif" } resolution = 3.03 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= -0.000 sd= 0.007 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 P 8 5.49 5 S 21 5.16 5 C 2602 2.51 5 N 677 2.21 5 O 780 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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4088 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2164 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 273} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 934 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 118} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 868 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 7, 'TRANS': 119} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 3, 'GLU:plan': 3, 'ASP:plan': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 65 Chain: "A" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 122 Unusual residues: {'CDL': 3, 'UTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 220 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-4': 2, 'CDL:plan-1': 2, 'CDL:plan-2': 1} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 1.21, per 1000 atoms: 0.30 Number of scatterers: 4088 At special positions: 0 Unit cell: (63.855, 66.435, 127.71, 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) S 21 16.00 P 8 15.00 O 780 8.00 N 677 7.00 C 2602 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 98 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 105.9 milliseconds 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 974 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 6 sheets defined 52.2% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 10 through 47 removed outlier: 3.951A pdb=" N GLY A 14 " --> pdb=" O HIS A 10 " (cutoff:3.500A) Proline residue: A 33 - end of helix removed outlier: 4.091A pdb=" N GLY A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU A 46 " --> pdb=" O GLN A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 69 Processing helix chain 'A' and resid 70 through 76 removed outlier: 3.905A pdb=" N LEU A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 95 removed outlier: 3.785A pdb=" N SER A 90 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 111 through 144 Proline residue: A 133 - end of helix Processing helix chain 'A' and resid 156 through 173 removed outlier: 6.935A pdb=" N LEU A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 9.061A pdb=" N THR A 171 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 173 " --> pdb=" O GLY A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 205 removed outlier: 3.545A pdb=" N ASN A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 243 Proline residue: A 232 - end of helix Processing helix chain 'A' and resid 250 through 262 Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 270 through 298 Processing helix chain 'B' and resid 31 through 35 Processing helix chain 'B' and resid 90 through 94 Processing helix chain 'B' and resid 110 through 114 Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 108 through 118 removed outlier: 5.450A pdb=" N THR C 115 " --> pdb=" O TYR C 112 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ALA C 116 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 10 Processing sheet with id=AA2, first strand: chain 'B' and resid 13 through 14 removed outlier: 6.422A pdb=" N GLY B 13 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ARG B 41 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N PHE B 50 " --> pdb=" O ARG B 41 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 13 through 14 removed outlier: 6.422A pdb=" N GLY B 13 " --> pdb=" O THR B 124 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 6 through 10 Processing sheet with id=AA5, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.448A pdb=" N GLY C 13 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ARG C 41 " --> pdb=" O PHE C 50 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N PHE C 50 " --> pdb=" O ARG C 41 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.448A pdb=" N GLY C 13 " --> pdb=" O THR C 128 " (cutoff:3.500A) 282 hydrogen bonds defined for protein. 744 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: 0.42 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 662 1.32 - 1.44: 1130 1.44 - 1.57: 2340 1.57 - 1.69: 15 1.69 - 1.81: 31 Bond restraints: 4178 Sorted by residual: bond pdb=" O3B UTP A 401 " pdb=" PG UTP A 401 " ideal model delta sigma weight residual 1.726 1.602 0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" OB5 CDL A 404 " pdb=" PB2 CDL A 404 " ideal model delta sigma weight residual 1.657 1.568 0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" OB5 CDL A 403 " pdb=" PB2 CDL A 403 " ideal model delta sigma weight residual 1.657 1.572 0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" OA5 CDL A 402 " pdb=" PA1 CDL A 402 " ideal model delta sigma weight residual 1.651 1.573 0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" OA5 CDL A 403 " pdb=" PA1 CDL A 403 " ideal model delta sigma weight residual 1.651 1.577 0.074 2.00e-02 2.50e+03 1.36e+01 ... (remaining 4173 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 5489 2.08 - 4.17: 165 4.17 - 6.25: 33 6.25 - 8.33: 4 8.33 - 10.42: 1 Bond angle restraints: 5692 Sorted by residual: angle pdb=" N GLY B 104 " pdb=" CA GLY B 104 " pdb=" C GLY B 104 " ideal model delta sigma weight residual 110.87 104.80 6.07 1.54e+00 4.22e-01 1.55e+01 angle pdb=" PB UTP A 401 " pdb=" O3B UTP A 401 " pdb=" PG UTP A 401 " ideal model delta sigma weight residual 127.83 138.25 -10.42 3.00e+00 1.11e-01 1.21e+01 angle pdb=" CA TYR B 106 " pdb=" CB TYR B 106 " pdb=" CG TYR B 106 " ideal model delta sigma weight residual 113.90 107.78 6.12 1.80e+00 3.09e-01 1.15e+01 angle pdb=" C GLY B 104 " pdb=" N GLY B 105 " pdb=" CA GLY B 105 " ideal model delta sigma weight residual 120.79 115.18 5.61 1.78e+00 3.16e-01 9.94e+00 angle pdb=" CA TYR A 75 " pdb=" CB TYR A 75 " pdb=" CG TYR A 75 " ideal model delta sigma weight residual 113.90 108.27 5.63 1.80e+00 3.09e-01 9.79e+00 ... (remaining 5687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.65: 2280 15.65 - 31.29: 136 31.29 - 46.94: 61 46.94 - 62.58: 35 62.58 - 78.23: 5 Dihedral angle restraints: 2517 sinusoidal: 982 harmonic: 1535 Sorted by residual: dihedral pdb=" CD ARG A 153 " pdb=" NE ARG A 153 " pdb=" CZ ARG A 153 " pdb=" NH1 ARG A 153 " ideal model delta sinusoidal sigma weight residual 0.00 50.62 -50.62 1 1.00e+01 1.00e-02 3.51e+01 dihedral pdb=" CA HIS A 148 " pdb=" C HIS A 148 " pdb=" N GLY A 149 " pdb=" CA GLY A 149 " ideal model delta harmonic sigma weight residual 180.00 156.21 23.79 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA GLY A 77 " pdb=" C GLY A 77 " pdb=" N LEU A 78 " pdb=" CA LEU A 78 " ideal model delta harmonic sigma weight residual -180.00 -159.75 -20.25 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 2514 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 513 0.056 - 0.112: 95 0.112 - 0.168: 27 0.168 - 0.224: 4 0.224 - 0.280: 1 Chirality restraints: 640 Sorted by residual: chirality pdb=" CA PHE A 268 " pdb=" N PHE A 268 " pdb=" C PHE A 268 " pdb=" CB PHE A 268 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA GLN A 132 " pdb=" N GLN A 132 " pdb=" C GLN A 132 " pdb=" CB GLN A 132 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA TYR A 75 " pdb=" N TYR A 75 " pdb=" C TYR A 75 " pdb=" CB TYR A 75 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.72e-01 ... (remaining 637 not shown) Planarity restraints: 715 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 153 " 0.667 9.50e-02 1.11e+02 3.01e-01 6.77e+01 pdb=" NE ARG A 153 " -0.062 2.00e-02 2.50e+03 pdb=" CZ ARG A 153 " 0.055 2.00e-02 2.50e+03 pdb=" NH1 ARG A 153 " -0.022 2.00e-02 2.50e+03 pdb=" NH2 ARG A 153 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 239 " -0.202 9.50e-02 1.11e+02 9.11e-02 6.23e+00 pdb=" NE ARG A 239 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG A 239 " -0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG A 239 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 239 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 268 " -0.022 2.00e-02 2.50e+03 1.78e-02 5.53e+00 pdb=" CG PHE A 268 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE A 268 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 268 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 268 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 268 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 268 " -0.004 2.00e-02 2.50e+03 ... (remaining 712 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 640 2.76 - 3.30: 3965 3.30 - 3.83: 7156 3.83 - 4.37: 8401 4.37 - 4.90: 14677 Nonbonded interactions: 34839 Sorted by model distance: nonbonded pdb=" O SER B 108 " pdb=" OH TYR B 114 " model vdw 2.226 3.040 nonbonded pdb=" OE1 GLU A 135 " pdb=" ND2 ASN A 180 " model vdw 2.245 3.120 nonbonded pdb=" OE1 GLU A 262 " pdb=" NZ LYS A 269 " model vdw 2.259 3.120 nonbonded pdb=" OE1 GLU A 46 " pdb=" OH TYR A 248 " model vdw 2.311 3.040 nonbonded pdb=" OE2 GLU A 69 " pdb=" OG SER A 145 " model vdw 2.367 3.040 ... (remaining 34834 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.500 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.610 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:0.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 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 : 0.008 0.124 4180 Z= 0.376 Angle : 0.874 10.417 5696 Z= 0.464 Chirality : 0.052 0.280 640 Planarity : 0.014 0.301 715 Dihedral : 14.445 78.229 1537 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 0.26 % Allowed : 0.77 % Favored : 98.98 % 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 are not related in a simple way. whole: 0.89 (0.33), residues: 534 helix: 0.70 (0.29), residues: 228 sheet: 0.23 (0.51), residues: 94 loop : 0.92 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.063 0.005 ARG A 153 TYR 0.030 0.004 TYR B 106 PHE 0.041 0.003 PHE A 268 TRP 0.026 0.003 TRP B 110 HIS 0.005 0.002 HIS A 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00830 / 0.38 ( 4178) covalent geometry : angle 0.87328 / 0.46 ( 5692) SS BOND : bond 0.00365 / 0.18 ( 2) SS BOND : angle 1.65989 / 0.86 ( 4) hydrogen bonds : bond 0.14353 / 9.09 ( 274) hydrogen bonds : angle 7.86295 / 5.66 ( 744) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.128 Fit side-chains REVERT: A 67 LYS cc_start: 0.7967 (mmtt) cc_final: 0.7454 (mmmt) outliers start: 1 outliers final: 0 residues processed: 46 average time/residue: 0.0520 time to fit residues: 3.1622 Evaluate side-chains 39 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.100 ------------------------------------------------------------------------------- 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: 0.0870 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.0770 chunk 16 optimal weight: 0.0980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 HIS A 242 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.197567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.160879 restraints weight = 3747.862| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 1.31 r_work: 0.3390 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4180 Z= 0.146 Angle : 0.572 6.552 5696 Z= 0.305 Chirality : 0.042 0.143 640 Planarity : 0.005 0.032 715 Dihedral : 13.091 59.746 727 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 0.26 % Allowed : 4.34 % Favored : 95.41 % 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 are not related in a simple way. whole: 2.24 (0.35), residues: 534 helix: 2.36 (0.31), residues: 223 sheet: 0.23 (0.50), residues: 93 loop : 1.34 (0.44), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 40 TYR 0.018 0.001 TYR B 106 PHE 0.012 0.002 PHE A 289 TRP 0.013 0.002 TRP C 39 HIS 0.003 0.001 HIS A 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 ( 4178) covalent geometry : angle 0.57223 / 0.31 ( 5692) SS BOND : bond 0.00181 / 0.09 ( 2) SS BOND : angle 0.81069 / 0.47 ( 4) hydrogen bonds : bond 0.04476 / 2.97 ( 274) hydrogen bonds : angle 5.49244 / 4.01 ( 744) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.146 Fit side-chains REVERT: A 67 LYS cc_start: 0.8237 (mmtt) cc_final: 0.7785 (mmmt) REVERT: A 103 LEU cc_start: 0.7315 (mp) cc_final: 0.6861 (mp) outliers start: 1 outliers final: 1 residues processed: 46 average time/residue: 0.0548 time to fit residues: 3.4827 Evaluate side-chains 42 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 27 optimal weight: 0.9980 chunk 25 optimal weight: 0.0980 chunk 45 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.190890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.155677 restraints weight = 3770.077| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 1.27 r_work: 0.3336 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4180 Z= 0.191 Angle : 0.582 6.109 5696 Z= 0.306 Chirality : 0.042 0.156 640 Planarity : 0.005 0.060 715 Dihedral : 12.225 58.233 727 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.79 % Allowed : 4.85 % Favored : 93.37 % 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 are not related in a simple way. whole: 2.14 (0.35), residues: 534 helix: 2.33 (0.31), residues: 223 sheet: 0.32 (0.51), residues: 91 loop : 1.13 (0.42), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 102 TYR 0.015 0.001 TYR B 106 PHE 0.020 0.002 PHE A 268 TRP 0.020 0.002 TRP C 39 HIS 0.003 0.001 HIS A 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 ( 4178) covalent geometry : angle 0.58069 / 0.31 ( 5692) SS BOND : bond 0.00358 / 0.17 ( 2) SS BOND : angle 1.75131 / 1.00 ( 4) hydrogen bonds : bond 0.04465 / 2.89 ( 274) hydrogen bonds : angle 5.49260 / 4.03 ( 744) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.194 Fit side-chains REVERT: A 67 LYS cc_start: 0.8252 (mmtt) cc_final: 0.7784 (mmmt) REVERT: A 103 LEU cc_start: 0.7292 (mp) cc_final: 0.6895 (mp) REVERT: A 198 MET cc_start: 0.7288 (tpp) cc_final: 0.6778 (mmt) outliers start: 7 outliers final: 7 residues processed: 48 average time/residue: 0.0552 time to fit residues: 3.7348 Evaluate side-chains 49 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 124 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 35 optimal weight: 0.0970 chunk 34 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.192596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.156421 restraints weight = 3676.555| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.35 r_work: 0.3378 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4180 Z= 0.173 Angle : 0.553 6.171 5696 Z= 0.288 Chirality : 0.041 0.141 640 Planarity : 0.005 0.048 715 Dihedral : 11.977 59.930 727 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.79 % Allowed : 6.12 % Favored : 92.09 % 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 are not related in a simple way. whole: 2.09 (0.35), residues: 534 helix: 2.35 (0.31), residues: 223 sheet: 0.37 (0.52), residues: 90 loop : 1.00 (0.42), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 41 TYR 0.011 0.001 TYR A 75 PHE 0.013 0.002 PHE A 268 TRP 0.016 0.001 TRP C 39 HIS 0.002 0.001 HIS B 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 ( 4178) covalent geometry : angle 0.55140 / 0.29 ( 5692) SS BOND : bond 0.00384 / 0.20 ( 2) SS BOND : angle 1.47553 / 0.85 ( 4) hydrogen bonds : bond 0.04159 / 2.72 ( 274) hydrogen bonds : angle 5.37793 / 3.94 ( 744) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.092 Fit side-chains REVERT: A 67 LYS cc_start: 0.8255 (mmtt) cc_final: 0.7800 (mmmt) REVERT: A 130 ILE cc_start: 0.8633 (mt) cc_final: 0.8380 (mm) REVERT: A 171 THR cc_start: 0.8095 (t) cc_final: 0.7884 (m) REVERT: A 198 MET cc_start: 0.7346 (tpp) cc_final: 0.6847 (mmt) REVERT: A 229 MET cc_start: 0.8482 (mmm) cc_final: 0.8220 (mmm) outliers start: 7 outliers final: 7 residues processed: 48 average time/residue: 0.0416 time to fit residues: 2.7392 Evaluate side-chains 50 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 80 ASN Chi-restraints excluded: chain B residue 124 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 44 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 0.0980 chunk 22 optimal weight: 0.0770 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 0.2980 chunk 37 optimal weight: 0.9980 chunk 26 optimal weight: 0.0770 chunk 18 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.2296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.194493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.156451 restraints weight = 3697.176| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.52 r_work: 0.3344 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4180 Z= 0.120 Angle : 0.500 6.013 5696 Z= 0.261 Chirality : 0.039 0.150 640 Planarity : 0.004 0.032 715 Dihedral : 11.567 59.137 727 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.04 % Allowed : 6.12 % Favored : 91.84 % 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 are not related in a simple way. whole: 2.31 (0.35), residues: 534 helix: 2.60 (0.32), residues: 224 sheet: 0.51 (0.53), residues: 90 loop : 0.99 (0.42), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 75 TYR 0.010 0.001 TYR A 158 PHE 0.010 0.001 PHE A 289 TRP 0.016 0.001 TRP C 39 HIS 0.001 0.000 HIS A 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 4178) covalent geometry : angle 0.49984 / 0.26 ( 5692) SS BOND : bond 0.00115 / 0.06 ( 2) SS BOND : angle 0.73870 / 0.43 ( 4) hydrogen bonds : bond 0.03745 / 2.46 ( 274) hydrogen bonds : angle 5.16170 / 3.78 ( 744) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.144 Fit side-chains REVERT: A 67 LYS cc_start: 0.8082 (mmtt) cc_final: 0.7639 (mmmt) REVERT: A 88 SER cc_start: 0.8192 (t) cc_final: 0.7850 (m) REVERT: A 103 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6810 (mp) REVERT: A 130 ILE cc_start: 0.8632 (mt) cc_final: 0.8401 (mm) REVERT: A 198 MET cc_start: 0.7205 (tpp) cc_final: 0.6735 (mmt) REVERT: A 229 MET cc_start: 0.8469 (mmm) cc_final: 0.8228 (mmm) outliers start: 8 outliers final: 5 residues processed: 52 average time/residue: 0.0528 time to fit residues: 3.8406 Evaluate side-chains 50 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 124 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 41 optimal weight: 4.9990 chunk 26 optimal weight: 0.2980 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 0.0980 chunk 45 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 11 optimal weight: 0.0970 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.193526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.153053 restraints weight = 3740.950| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.39 r_work: 0.3355 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4180 Z= 0.153 Angle : 0.521 6.095 5696 Z= 0.271 Chirality : 0.040 0.142 640 Planarity : 0.004 0.041 715 Dihedral : 10.512 58.914 727 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.30 % Allowed : 6.89 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.35), residues: 534 helix: 2.50 (0.32), residues: 224 sheet: 0.17 (0.53), residues: 84 loop : 0.85 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 84 TYR 0.010 0.001 TYR A 158 PHE 0.012 0.001 PHE A 268 TRP 0.016 0.001 TRP C 39 HIS 0.002 0.001 HIS B 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 4178) covalent geometry : angle 0.52061 / 0.27 ( 5692) SS BOND : bond 0.00239 / 0.12 ( 2) SS BOND : angle 0.95620 / 0.54 ( 4) hydrogen bonds : bond 0.03865 / 2.51 ( 274) hydrogen bonds : angle 5.18723 / 3.81 ( 744) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.187 Fit side-chains REVERT: A 67 LYS cc_start: 0.8072 (mmtt) cc_final: 0.7646 (mmmt) REVERT: A 103 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6842 (mp) REVERT: A 198 MET cc_start: 0.7228 (tpp) cc_final: 0.6795 (mmt) REVERT: A 229 MET cc_start: 0.8435 (mmm) cc_final: 0.8150 (mmm) outliers start: 9 outliers final: 7 residues processed: 48 average time/residue: 0.0530 time to fit residues: 3.5868 Evaluate side-chains 50 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 124 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 3 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.191021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.152667 restraints weight = 3773.475| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.40 r_work: 0.3400 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 4180 Z= 0.216 Angle : 0.579 6.415 5696 Z= 0.299 Chirality : 0.042 0.142 640 Planarity : 0.005 0.056 715 Dihedral : 10.432 54.776 727 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.04 % Allowed : 8.16 % Favored : 89.80 % 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 are not related in a simple way. whole: 1.76 (0.35), residues: 534 helix: 2.15 (0.32), residues: 224 sheet: 0.10 (0.54), residues: 84 loop : 0.74 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 84 TYR 0.013 0.001 TYR A 75 PHE 0.015 0.002 PHE A 268 TRP 0.013 0.002 TRP C 39 HIS 0.003 0.001 HIS B 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.22 ( 4178) covalent geometry : angle 0.57835 / 0.30 ( 5692) SS BOND : bond 0.00229 / 0.11 ( 2) SS BOND : angle 1.23855 / 0.71 ( 4) hydrogen bonds : bond 0.04375 / 2.84 ( 274) hydrogen bonds : angle 5.43780 / 4.01 ( 744) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.161 Fit side-chains REVERT: A 67 LYS cc_start: 0.8138 (mmtt) cc_final: 0.7686 (mmmt) REVERT: A 103 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.6967 (mp) REVERT: A 130 ILE cc_start: 0.8642 (mt) cc_final: 0.8398 (mm) REVERT: A 198 MET cc_start: 0.7327 (tpp) cc_final: 0.6885 (mmt) REVERT: A 229 MET cc_start: 0.8481 (mmm) cc_final: 0.8265 (mmm) outliers start: 8 outliers final: 7 residues processed: 49 average time/residue: 0.0519 time to fit residues: 3.5674 Evaluate side-chains 52 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 124 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 34 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 48 optimal weight: 0.0170 chunk 40 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 2 optimal weight: 0.0980 chunk 1 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.192756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.155347 restraints weight = 3712.687| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 1.33 r_work: 0.3410 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 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 : 0.004 0.044 4180 Z= 0.152 Angle : 0.529 6.478 5696 Z= 0.272 Chirality : 0.040 0.170 640 Planarity : 0.004 0.036 715 Dihedral : 10.114 54.761 727 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.30 % Allowed : 8.16 % Favored : 89.54 % 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 are not related in a simple way. whole: 1.90 (0.35), residues: 534 helix: 2.35 (0.32), residues: 225 sheet: 0.10 (0.54), residues: 83 loop : 0.74 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 84 TYR 0.011 0.001 TYR A 75 PHE 0.010 0.001 PHE A 289 TRP 0.012 0.001 TRP C 39 HIS 0.002 0.001 HIS B 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 4178) covalent geometry : angle 0.52847 / 0.27 ( 5692) SS BOND : bond 0.00146 / 0.07 ( 2) SS BOND : angle 0.79264 / 0.45 ( 4) hydrogen bonds : bond 0.03890 / 2.53 ( 274) hydrogen bonds : angle 5.24814 / 3.87 ( 744) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.148 Fit side-chains REVERT: A 67 LYS cc_start: 0.8108 (mmtt) cc_final: 0.7684 (mmmt) REVERT: A 103 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.6965 (mp) REVERT: A 130 ILE cc_start: 0.8602 (mt) cc_final: 0.8364 (mm) REVERT: A 198 MET cc_start: 0.7269 (tpp) cc_final: 0.6853 (mmt) outliers start: 9 outliers final: 8 residues processed: 47 average time/residue: 0.0440 time to fit residues: 2.9436 Evaluate side-chains 51 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 124 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 13 optimal weight: 0.3980 chunk 44 optimal weight: 0.9980 chunk 26 optimal weight: 0.2980 chunk 36 optimal weight: 0.8980 chunk 12 optimal weight: 0.1980 chunk 42 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 38 optimal weight: 0.4980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.202130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.151860 restraints weight = 3701.912| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.68 r_work: 0.3336 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4180 Z= 0.141 Angle : 0.514 6.077 5696 Z= 0.264 Chirality : 0.039 0.137 640 Planarity : 0.004 0.032 715 Dihedral : 9.877 57.570 727 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.04 % Allowed : 8.67 % Favored : 89.29 % 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 are not related in a simple way. whole: 2.01 (0.35), residues: 534 helix: 2.48 (0.32), residues: 225 sheet: 0.15 (0.55), residues: 82 loop : 0.74 (0.40), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 84 TYR 0.010 0.001 TYR A 158 PHE 0.011 0.001 PHE A 289 TRP 0.020 0.001 TRP C 39 HIS 0.002 0.001 HIS B 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 4178) covalent geometry : angle 0.51329 / 0.26 ( 5692) SS BOND : bond 0.00149 / 0.07 ( 2) SS BOND : angle 0.76552 / 0.43 ( 4) hydrogen bonds : bond 0.03735 / 2.43 ( 274) hydrogen bonds : angle 5.18499 / 3.83 ( 744) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.143 Fit side-chains REVERT: A 67 LYS cc_start: 0.8056 (mmtt) cc_final: 0.7620 (mmmt) REVERT: A 103 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6898 (mp) REVERT: A 130 ILE cc_start: 0.8569 (mt) cc_final: 0.8328 (mm) REVERT: A 198 MET cc_start: 0.7248 (tpp) cc_final: 0.6856 (mmt) outliers start: 8 outliers final: 7 residues processed: 45 average time/residue: 0.0526 time to fit residues: 3.3438 Evaluate side-chains 49 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 124 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 0.3980 chunk 2 optimal weight: 0.0870 chunk 39 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 13 optimal weight: 0.0970 chunk 24 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.194494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.156843 restraints weight = 3680.675| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.29 r_work: 0.3445 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4180 Z= 0.135 Angle : 0.511 6.035 5696 Z= 0.262 Chirality : 0.040 0.190 640 Planarity : 0.004 0.030 715 Dihedral : 9.788 59.805 727 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.04 % Allowed : 8.93 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.35), residues: 534 helix: 2.53 (0.32), residues: 225 sheet: 0.15 (0.54), residues: 82 loop : 0.76 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 84 TYR 0.009 0.001 TYR A 158 PHE 0.010 0.001 PHE A 289 TRP 0.016 0.001 TRP C 39 HIS 0.002 0.001 HIS B 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 4178) covalent geometry : angle 0.51100 / 0.26 ( 5692) SS BOND : bond 0.00079 / 0.04 ( 2) SS BOND : angle 0.72272 / 0.42 ( 4) hydrogen bonds : bond 0.03681 / 2.40 ( 274) hydrogen bonds : angle 5.15380 / 3.81 ( 744) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.184 Fit side-chains REVERT: A 67 LYS cc_start: 0.8074 (mmtt) cc_final: 0.7655 (mmmt) REVERT: A 103 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.7015 (mp) REVERT: A 130 ILE cc_start: 0.8552 (mt) cc_final: 0.8323 (mm) REVERT: A 198 MET cc_start: 0.7256 (tpp) cc_final: 0.6890 (mmt) outliers start: 8 outliers final: 7 residues processed: 46 average time/residue: 0.0551 time to fit residues: 3.5581 Evaluate side-chains 50 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 124 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 14 optimal weight: 0.0270 chunk 7 optimal weight: 0.9980 chunk 46 optimal weight: 0.0980 chunk 17 optimal weight: 0.0870 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 12 optimal weight: 0.2980 chunk 15 optimal weight: 0.2980 overall best weight: 0.1616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.199928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.161516 restraints weight = 3714.455| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 1.53 r_work: 0.3392 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4180 Z= 0.105 Angle : 0.480 5.884 5696 Z= 0.245 Chirality : 0.038 0.133 640 Planarity : 0.004 0.030 715 Dihedral : 9.415 59.018 727 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 1.53 % Allowed : 9.69 % Favored : 88.78 % 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 are not related in a simple way. whole: 2.30 (0.35), residues: 534 helix: 2.80 (0.32), residues: 225 sheet: 0.23 (0.54), residues: 82 loop : 0.84 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 84 TYR 0.009 0.001 TYR B 106 PHE 0.007 0.001 PHE A 32 TRP 0.020 0.001 TRP C 39 HIS 0.000 0.000 HIS B 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 ( 4178) covalent geometry : angle 0.47967 / 0.25 ( 5692) SS BOND : bond 0.00053 / 0.03 ( 2) SS BOND : angle 0.56284 / 0.32 ( 4) hydrogen bonds : bond 0.03336 / 2.19 ( 274) hydrogen bonds : angle 4.96088 / 3.66 ( 744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1597.22 seconds wall clock time: 28 minutes 4.42 seconds (1684.42 seconds total)