Starting phenix.real_space_refine on Tue Feb 11 08:58:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yjp_39345/02_2025/8yjp_39345.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yjp_39345/02_2025/8yjp_39345.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yjp_39345/02_2025/8yjp_39345.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yjp_39345/02_2025/8yjp_39345.map" model { file = "/net/cci-nas-00/data/ceres_data/8yjp_39345/02_2025/8yjp_39345.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yjp_39345/02_2025/8yjp_39345.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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 4 5.49 5 S 34 5.16 5 C 3359 2.51 5 N 726 2.21 5 O 823 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4946 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2241 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 10, 'TRANS': 287} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2241 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 10, 'TRANS': 287} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 246 Unusual residues: {'CLR': 5, 'MW9': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 218 Unusual residues: {'CLR': 4, 'MW9': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 3.65, per 1000 atoms: 0.74 Number of scatterers: 4946 At special positions: 0 Unit cell: (66.96, 79.98, 95.79, 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 34 16.00 P 4 15.00 O 823 8.00 N 726 7.00 C 3359 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 191 " - pdb=" SG CYS A 216 " distance=2.44 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 582.9 milliseconds 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1112 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 1 sheets defined 77.0% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 23 through 34 removed outlier: 3.610A pdb=" N LYS A 29 " --> pdb=" O HIS A 25 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER A 34 " --> pdb=" O THR A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 74 Processing helix chain 'A' and resid 77 through 83 Processing helix chain 'A' and resid 84 through 106 removed outlier: 3.676A pdb=" N GLY A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 150 removed outlier: 4.011A pdb=" N THR A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) Proline residue: A 137 - end of helix Processing helix chain 'A' and resid 161 through 187 removed outlier: 3.966A pdb=" N LEU A 165 " --> pdb=" O LYS A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 246 Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.857A pdb=" N GLN A 256 " --> pdb=" O PRO A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 281 Processing helix chain 'A' and resid 284 through 319 Proline residue: A 310 - end of helix Processing helix chain 'B' and resid 23 through 34 removed outlier: 3.934A pdb=" N LEU B 27 " --> pdb=" O PRO B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 74 Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 84 through 106 removed outlier: 3.804A pdb=" N GLY B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 151 removed outlier: 3.862A pdb=" N THR B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) Proline residue: B 137 - end of helix Processing helix chain 'B' and resid 161 through 187 removed outlier: 3.880A pdb=" N LEU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 246 Processing helix chain 'B' and resid 251 through 256 removed outlier: 3.860A pdb=" N GLN B 256 " --> pdb=" O PRO B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 281 Processing helix chain 'B' and resid 284 through 319 Proline residue: B 310 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 216 removed outlier: 3.556A pdb=" N PHE A 215 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 192 " --> pdb=" O PHE A 215 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 195 " --> pdb=" O MET B 199 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 197 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B 197 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET A 199 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU B 195 " --> pdb=" O MET A 199 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN B 193 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA B 217 " --> pdb=" O GLN B 190 " (cutoff:3.500A) 376 hydrogen bonds defined for protein. 1122 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.40 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 680 1.31 - 1.44: 1267 1.44 - 1.56: 3060 1.56 - 1.69: 8 1.69 - 1.82: 48 Bond restraints: 5063 Sorted by residual: bond pdb=" C8 MW9 A 402 " pdb=" C9 MW9 A 402 " ideal model delta sigma weight residual 1.548 1.332 0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C8 MW9 B 404 " pdb=" C9 MW9 B 404 " ideal model delta sigma weight residual 1.548 1.333 0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C8 MW9 B 403 " pdb=" C9 MW9 B 403 " ideal model delta sigma weight residual 1.548 1.335 0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C8 MW9 A 401 " pdb=" C9 MW9 A 401 " ideal model delta sigma weight residual 1.548 1.336 0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C24 MW9 A 402 " pdb=" O8 MW9 A 402 " ideal model delta sigma weight residual 1.342 1.417 -0.075 2.00e-02 2.50e+03 1.41e+01 ... (remaining 5058 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.73: 6831 5.73 - 11.47: 63 11.47 - 17.20: 12 17.20 - 22.94: 0 22.94 - 28.67: 4 Bond angle restraints: 6910 Sorted by residual: angle pdb=" C32 MW9 B 403 " pdb=" C33 MW9 B 403 " pdb=" C34 MW9 B 403 " ideal model delta sigma weight residual 125.32 153.99 -28.67 3.00e+00 1.11e-01 9.13e+01 angle pdb=" C32 MW9 A 402 " pdb=" C33 MW9 A 402 " pdb=" C34 MW9 A 402 " ideal model delta sigma weight residual 125.32 153.33 -28.01 3.00e+00 1.11e-01 8.72e+01 angle pdb=" C32 MW9 B 404 " pdb=" C33 MW9 B 404 " pdb=" C34 MW9 B 404 " ideal model delta sigma weight residual 125.32 153.03 -27.71 3.00e+00 1.11e-01 8.53e+01 angle pdb=" C32 MW9 A 401 " pdb=" C33 MW9 A 401 " pdb=" C34 MW9 A 401 " ideal model delta sigma weight residual 125.32 152.94 -27.62 3.00e+00 1.11e-01 8.48e+01 angle pdb=" C SER B 251 " pdb=" N PRO B 252 " pdb=" CA PRO B 252 " ideal model delta sigma weight residual 120.38 113.44 6.94 1.03e+00 9.43e-01 4.53e+01 ... (remaining 6905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.62: 3319 35.62 - 71.24: 121 71.24 - 106.86: 27 106.86 - 142.48: 10 142.48 - 178.09: 9 Dihedral angle restraints: 3486 sinusoidal: 1766 harmonic: 1720 Sorted by residual: dihedral pdb=" C20 MW9 A 402 " pdb=" O2 MW9 A 402 " pdb=" P MW9 A 402 " pdb=" O5 MW9 A 402 " ideal model delta sinusoidal sigma weight residual 301.77 123.68 178.09 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C11 MW9 B 403 " pdb=" C10 MW9 B 403 " pdb=" C9 MW9 B 403 " pdb=" C8 MW9 B 403 " ideal model delta sinusoidal sigma weight residual -59.86 114.41 -174.27 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O MW9 A 401 " pdb=" C16 MW9 A 401 " pdb=" C17 MW9 A 401 " pdb=" C15 MW9 A 401 " ideal model delta sinusoidal sigma weight residual 102.59 -90.28 -167.13 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 3483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 792 0.105 - 0.210: 56 0.210 - 0.315: 9 0.315 - 0.420: 11 0.420 - 0.525: 4 Chirality restraints: 872 Sorted by residual: chirality pdb=" C14 CLR B 405 " pdb=" C13 CLR B 405 " pdb=" C15 CLR B 405 " pdb=" C8 CLR B 405 " both_signs ideal model delta sigma weight residual False -2.32 -2.84 0.52 2.00e-01 2.50e+01 6.88e+00 chirality pdb=" C14 CLR B 406 " pdb=" C13 CLR B 406 " pdb=" C15 CLR B 406 " pdb=" C8 CLR B 406 " both_signs ideal model delta sigma weight residual False -2.32 -2.84 0.52 2.00e-01 2.50e+01 6.87e+00 chirality pdb=" C14 CLR A 407 " pdb=" C13 CLR A 407 " pdb=" C15 CLR A 407 " pdb=" C8 CLR A 407 " both_signs ideal model delta sigma weight residual False -2.32 -2.84 0.52 2.00e-01 2.50e+01 6.84e+00 ... (remaining 869 not shown) Planarity restraints: 754 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 148 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.04e+00 pdb=" C VAL A 148 " -0.049 2.00e-02 2.50e+03 pdb=" O VAL A 148 " 0.018 2.00e-02 2.50e+03 pdb=" N PHE A 149 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 229 " 0.017 2.00e-02 2.50e+03 1.76e-02 7.70e+00 pdb=" CG TRP A 229 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP A 229 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 229 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 229 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 229 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 229 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 229 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 229 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 229 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 147 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.76e+00 pdb=" C LYS B 147 " -0.045 2.00e-02 2.50e+03 pdb=" O LYS B 147 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL B 148 " 0.015 2.00e-02 2.50e+03 ... (remaining 751 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 883 2.77 - 3.30: 4956 3.30 - 3.84: 8012 3.84 - 4.37: 9033 4.37 - 4.90: 15913 Nonbonded interactions: 38797 Sorted by model distance: nonbonded pdb=" OG SER B 132 " pdb=" OD2 ASP B 176 " model vdw 2.240 3.040 nonbonded pdb=" O LYS A 76 " pdb=" NZ LYS A 81 " model vdw 2.260 3.120 nonbonded pdb=" OG SER A 218 " pdb=" O MW9 A 402 " model vdw 2.267 3.040 nonbonded pdb=" O VAL B 298 " pdb=" OG1 THR B 302 " model vdw 2.278 3.040 nonbonded pdb=" O THR B 98 " pdb=" OG SER B 101 " model vdw 2.292 3.040 ... (remaining 38792 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 22 through 319 or resid 405 through 406)) selection = (chain 'B' and (resid 22 through 319 or resid 405 through 406)) } 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: 0.960 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.780 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 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 : 0.009 0.216 5063 Z= 0.607 Angle : 1.465 28.669 6910 Z= 0.569 Chirality : 0.079 0.525 872 Planarity : 0.005 0.042 754 Dihedral : 22.112 178.095 2371 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.35), residues: 592 helix: 2.09 (0.24), residues: 436 sheet: 1.50 (0.83), residues: 36 loop : -3.36 (0.50), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 229 HIS 0.001 0.000 HIS B 73 PHE 0.008 0.002 PHE B 105 TYR 0.015 0.002 TYR A 241 ARG 0.003 0.000 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.463 Fit side-chains REVERT: A 265 ASN cc_start: 0.7159 (m-40) cc_final: 0.6933 (m110) REVERT: B 194 ILE cc_start: 0.7669 (pt) cc_final: 0.7456 (pt) REVERT: B 265 ASN cc_start: 0.7141 (m-40) cc_final: 0.6823 (m110) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1605 time to fit residues: 22.9524 Evaluate side-chains 100 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 304 ASN B 121 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.172984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.147181 restraints weight = 6455.247| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 1.98 r_work: 0.3802 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3629 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 5063 Z= 0.273 Angle : 0.687 8.856 6910 Z= 0.320 Chirality : 0.044 0.155 872 Planarity : 0.005 0.042 754 Dihedral : 22.843 179.182 1433 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.61 % Allowed : 10.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.34), residues: 592 helix: 2.38 (0.23), residues: 438 sheet: 1.43 (0.85), residues: 32 loop : -3.25 (0.46), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 229 HIS 0.001 0.000 HIS B 73 PHE 0.011 0.002 PHE B 105 TYR 0.014 0.002 TYR A 241 ARG 0.001 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 99 time to evaluate : 0.513 Fit side-chains REVERT: A 265 ASN cc_start: 0.7987 (m-40) cc_final: 0.7773 (m110) REVERT: B 82 MET cc_start: 0.7807 (mmm) cc_final: 0.7498 (mmm) REVERT: B 118 THR cc_start: 0.7983 (m) cc_final: 0.7782 (t) REVERT: B 194 ILE cc_start: 0.7959 (pt) cc_final: 0.7741 (pt) REVERT: B 265 ASN cc_start: 0.8081 (m-40) cc_final: 0.7766 (m110) outliers start: 3 outliers final: 2 residues processed: 100 average time/residue: 0.1579 time to fit residues: 20.6318 Evaluate side-chains 96 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 94 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain B residue 166 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 39 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 1 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 55 optimal weight: 0.0270 chunk 27 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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 = 0.4254 r_free = 0.4254 target = 0.172647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.146462 restraints weight = 6426.240| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 2.06 r_work: 0.3797 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5063 Z= 0.236 Angle : 0.620 10.603 6910 Z= 0.294 Chirality : 0.042 0.138 872 Planarity : 0.005 0.043 754 Dihedral : 20.688 178.986 1433 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.84 % Allowed : 13.27 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.34), residues: 592 helix: 2.56 (0.23), residues: 438 sheet: 1.83 (0.85), residues: 32 loop : -3.22 (0.46), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 229 HIS 0.002 0.001 HIS B 214 PHE 0.020 0.002 PHE B 275 TYR 0.024 0.002 TYR A 241 ARG 0.002 0.000 ARG B 279 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.492 Fit side-chains REVERT: A 172 LEU cc_start: 0.8269 (tt) cc_final: 0.7822 (tp) REVERT: A 265 ASN cc_start: 0.8017 (m-40) cc_final: 0.7773 (m110) REVERT: B 82 MET cc_start: 0.7899 (mmm) cc_final: 0.7571 (mmm) REVERT: B 118 THR cc_start: 0.7977 (m) cc_final: 0.7748 (t) REVERT: B 265 ASN cc_start: 0.8036 (m-40) cc_final: 0.7721 (m110) outliers start: 9 outliers final: 7 residues processed: 104 average time/residue: 0.1577 time to fit residues: 21.4546 Evaluate side-chains 104 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 174 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 43 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 1 optimal weight: 0.0470 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 0.0770 chunk 13 optimal weight: 0.0020 chunk 31 optimal weight: 0.8980 chunk 9 optimal weight: 0.0870 chunk 8 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 45 optimal weight: 0.0970 overall best weight: 0.0620 ------------------------------------------------------------------------------- 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 = 0.4292 r_free = 0.4292 target = 0.176025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.150777 restraints weight = 6528.284| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 2.10 r_work: 0.3847 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3674 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5063 Z= 0.141 Angle : 0.588 12.759 6910 Z= 0.276 Chirality : 0.039 0.134 872 Planarity : 0.004 0.041 754 Dihedral : 18.367 173.633 1433 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.84 % Allowed : 15.51 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.34), residues: 592 helix: 2.83 (0.23), residues: 428 sheet: 2.20 (0.90), residues: 32 loop : -2.90 (0.45), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 229 HIS 0.004 0.001 HIS B 214 PHE 0.031 0.001 PHE B 275 TYR 0.016 0.001 TYR A 241 ARG 0.001 0.000 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.530 Fit side-chains REVERT: A 99 TYR cc_start: 0.7375 (m-80) cc_final: 0.6882 (m-80) REVERT: A 107 ILE cc_start: 0.8374 (mt) cc_final: 0.8143 (mp) REVERT: A 172 LEU cc_start: 0.8201 (tt) cc_final: 0.7620 (tp) REVERT: B 67 PHE cc_start: 0.7184 (m-80) cc_final: 0.6965 (m-10) REVERT: B 118 THR cc_start: 0.7895 (m) cc_final: 0.7677 (t) REVERT: B 265 ASN cc_start: 0.8052 (m-40) cc_final: 0.7749 (m110) outliers start: 9 outliers final: 2 residues processed: 106 average time/residue: 0.1614 time to fit residues: 22.2243 Evaluate side-chains 99 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 199 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 15 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 29 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 311 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.171061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.145092 restraints weight = 6432.377| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 2.08 r_work: 0.3778 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5063 Z= 0.304 Angle : 0.637 8.464 6910 Z= 0.301 Chirality : 0.043 0.159 872 Planarity : 0.005 0.044 754 Dihedral : 18.334 179.230 1433 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.65 % Allowed : 16.73 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.34), residues: 592 helix: 2.70 (0.23), residues: 430 sheet: 2.13 (0.86), residues: 32 loop : -2.99 (0.46), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 229 HIS 0.002 0.001 HIS A 282 PHE 0.015 0.002 PHE B 275 TYR 0.014 0.002 TYR A 241 ARG 0.004 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.534 Fit side-chains REVERT: A 99 TYR cc_start: 0.7532 (m-80) cc_final: 0.7248 (m-80) REVERT: A 107 ILE cc_start: 0.8445 (mt) cc_final: 0.8205 (mp) REVERT: A 265 ASN cc_start: 0.8020 (m-40) cc_final: 0.7782 (m110) REVERT: B 99 TYR cc_start: 0.7570 (m-80) cc_final: 0.7370 (m-80) REVERT: B 265 ASN cc_start: 0.8072 (m-40) cc_final: 0.7733 (m110) outliers start: 13 outliers final: 8 residues processed: 106 average time/residue: 0.1472 time to fit residues: 20.7517 Evaluate side-chains 106 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 235 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 35 optimal weight: 0.0980 chunk 13 optimal weight: 0.0170 chunk 17 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 30 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.3618 ------------------------------------------------------------------------------- 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 = 0.4250 r_free = 0.4250 target = 0.172596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.147470 restraints weight = 6464.518| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 2.00 r_work: 0.3811 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5063 Z= 0.193 Angle : 0.595 9.011 6910 Z= 0.280 Chirality : 0.040 0.144 872 Planarity : 0.004 0.042 754 Dihedral : 17.900 178.081 1433 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.43 % Allowed : 19.18 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.34), residues: 592 helix: 2.84 (0.23), residues: 430 sheet: 2.47 (0.89), residues: 32 loop : -2.92 (0.46), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 315 HIS 0.002 0.001 HIS B 214 PHE 0.021 0.001 PHE B 275 TYR 0.013 0.001 TYR A 241 ARG 0.002 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.478 Fit side-chains REVERT: A 99 TYR cc_start: 0.7505 (m-80) cc_final: 0.6999 (m-80) REVERT: A 173 LEU cc_start: 0.8109 (mt) cc_final: 0.7907 (mt) REVERT: B 82 MET cc_start: 0.7874 (mmm) cc_final: 0.7546 (mmm) REVERT: B 265 ASN cc_start: 0.8041 (m-40) cc_final: 0.7711 (m110) outliers start: 7 outliers final: 4 residues processed: 97 average time/residue: 0.1553 time to fit residues: 19.6911 Evaluate side-chains 100 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 160 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 38 optimal weight: 0.7980 chunk 16 optimal weight: 0.0570 chunk 43 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 chunk 30 optimal weight: 20.0000 chunk 31 optimal weight: 0.3980 chunk 26 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 overall best weight: 0.4498 ------------------------------------------------------------------------------- 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 = 0.4245 r_free = 0.4245 target = 0.172067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.146760 restraints weight = 6381.422| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.05 r_work: 0.3800 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5063 Z= 0.213 Angle : 0.601 8.344 6910 Z= 0.284 Chirality : 0.041 0.147 872 Planarity : 0.004 0.042 754 Dihedral : 17.585 179.944 1433 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.84 % Allowed : 19.39 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.34), residues: 592 helix: 2.70 (0.23), residues: 442 sheet: 2.71 (0.89), residues: 32 loop : -3.18 (0.48), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 229 HIS 0.002 0.001 HIS B 214 PHE 0.020 0.002 PHE B 275 TYR 0.012 0.002 TYR A 241 ARG 0.002 0.000 ARG B 144 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.466 Fit side-chains REVERT: A 99 TYR cc_start: 0.7513 (m-80) cc_final: 0.7087 (m-80) REVERT: A 107 ILE cc_start: 0.8411 (mt) cc_final: 0.8174 (mp) REVERT: A 173 LEU cc_start: 0.8103 (mt) cc_final: 0.7899 (mt) REVERT: B 82 MET cc_start: 0.7947 (mmm) cc_final: 0.7553 (mmm) REVERT: B 105 PHE cc_start: 0.8207 (m-80) cc_final: 0.7994 (m-80) REVERT: B 147 LYS cc_start: 0.7846 (mmmm) cc_final: 0.7499 (mmmm) REVERT: B 265 ASN cc_start: 0.8058 (m-40) cc_final: 0.7733 (m110) REVERT: B 314 GLN cc_start: 0.6655 (OUTLIER) cc_final: 0.6433 (mp10) outliers start: 9 outliers final: 5 residues processed: 104 average time/residue: 0.2003 time to fit residues: 28.1392 Evaluate side-chains 105 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 314 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.0270 chunk 21 optimal weight: 0.5980 chunk 45 optimal weight: 0.0070 chunk 1 optimal weight: 20.0000 chunk 7 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.4456 ------------------------------------------------------------------------------- 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 = 0.4243 r_free = 0.4243 target = 0.171927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.146580 restraints weight = 6485.220| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 2.06 r_work: 0.3797 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5063 Z= 0.208 Angle : 0.604 9.148 6910 Z= 0.284 Chirality : 0.041 0.147 872 Planarity : 0.004 0.042 754 Dihedral : 17.312 178.029 1433 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.04 % Allowed : 20.00 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.34), residues: 592 helix: 2.84 (0.23), residues: 430 sheet: 2.85 (0.90), residues: 32 loop : -2.91 (0.47), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 315 HIS 0.002 0.000 HIS B 214 PHE 0.016 0.001 PHE B 275 TYR 0.025 0.002 TYR A 241 ARG 0.002 0.000 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.563 Fit side-chains REVERT: A 99 TYR cc_start: 0.7512 (m-80) cc_final: 0.7120 (m-80) REVERT: A 107 ILE cc_start: 0.8422 (mt) cc_final: 0.8196 (mp) REVERT: B 82 MET cc_start: 0.7979 (mmm) cc_final: 0.7575 (mmm) REVERT: B 105 PHE cc_start: 0.8187 (m-80) cc_final: 0.7985 (m-80) REVERT: B 147 LYS cc_start: 0.7853 (mmmm) cc_final: 0.7505 (mmmm) REVERT: B 265 ASN cc_start: 0.8064 (m-40) cc_final: 0.7757 (m110) REVERT: B 314 GLN cc_start: 0.6717 (OUTLIER) cc_final: 0.6515 (mp10) outliers start: 10 outliers final: 6 residues processed: 101 average time/residue: 0.2166 time to fit residues: 28.2632 Evaluate side-chains 103 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 314 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 18 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 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 = 0.4227 r_free = 0.4227 target = 0.170180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.144504 restraints weight = 6446.403| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 2.09 r_work: 0.3770 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3591 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 5063 Z= 0.305 Angle : 0.644 9.021 6910 Z= 0.304 Chirality : 0.044 0.178 872 Planarity : 0.005 0.043 754 Dihedral : 17.329 177.642 1433 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.45 % Allowed : 19.59 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.34), residues: 592 helix: 2.62 (0.23), residues: 430 sheet: 2.95 (0.89), residues: 32 loop : -2.92 (0.47), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 315 HIS 0.002 0.001 HIS A 282 PHE 0.014 0.002 PHE B 275 TYR 0.025 0.002 TYR A 241 ARG 0.003 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.525 Fit side-chains REVERT: A 99 TYR cc_start: 0.7530 (m-80) cc_final: 0.7111 (m-80) REVERT: A 107 ILE cc_start: 0.8446 (mt) cc_final: 0.8219 (mp) REVERT: A 265 ASN cc_start: 0.7959 (m-40) cc_final: 0.7740 (m110) REVERT: B 82 MET cc_start: 0.8014 (mmm) cc_final: 0.7608 (mmm) REVERT: B 105 PHE cc_start: 0.8304 (m-80) cc_final: 0.8002 (m-80) REVERT: B 147 LYS cc_start: 0.7862 (mmmm) cc_final: 0.7482 (mmmm) REVERT: B 265 ASN cc_start: 0.8058 (m-40) cc_final: 0.7727 (m110) REVERT: B 314 GLN cc_start: 0.6787 (OUTLIER) cc_final: 0.6552 (mp10) outliers start: 12 outliers final: 8 residues processed: 96 average time/residue: 0.1536 time to fit residues: 20.0068 Evaluate side-chains 99 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 314 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 42 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 6 optimal weight: 0.1980 chunk 21 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4238 r_free = 0.4238 target = 0.171380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.146536 restraints weight = 6491.298| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.02 r_work: 0.3787 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5063 Z= 0.230 Angle : 0.627 10.508 6910 Z= 0.298 Chirality : 0.042 0.171 872 Planarity : 0.005 0.043 754 Dihedral : 17.196 174.699 1433 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.84 % Allowed : 20.61 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.34), residues: 592 helix: 2.71 (0.23), residues: 430 sheet: 3.06 (0.88), residues: 32 loop : -2.89 (0.47), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 315 HIS 0.002 0.000 HIS B 214 PHE 0.013 0.001 PHE B 275 TYR 0.023 0.002 TYR A 241 ARG 0.002 0.000 ARG B 144 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.524 Fit side-chains REVERT: A 99 TYR cc_start: 0.7496 (m-80) cc_final: 0.7095 (m-80) REVERT: B 82 MET cc_start: 0.7947 (mmm) cc_final: 0.7560 (mmm) REVERT: B 147 LYS cc_start: 0.7808 (mmmm) cc_final: 0.7470 (mmmm) REVERT: B 265 ASN cc_start: 0.8067 (m-40) cc_final: 0.7753 (m110) REVERT: B 314 GLN cc_start: 0.6712 (OUTLIER) cc_final: 0.6495 (mp10) outliers start: 9 outliers final: 7 residues processed: 95 average time/residue: 0.1527 time to fit residues: 19.3863 Evaluate side-chains 99 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 314 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 24 optimal weight: 0.2980 chunk 8 optimal weight: 0.0050 chunk 13 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 31 optimal weight: 0.0980 chunk 56 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 overall best weight: 0.3394 ------------------------------------------------------------------------------- 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 = 0.4252 r_free = 0.4252 target = 0.172536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.147614 restraints weight = 6508.852| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.03 r_work: 0.3803 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3632 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5063 Z= 0.189 Angle : 0.605 9.989 6910 Z= 0.288 Chirality : 0.040 0.144 872 Planarity : 0.005 0.043 754 Dihedral : 16.976 173.224 1433 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.22 % Allowed : 21.22 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.34), residues: 592 helix: 2.82 (0.23), residues: 430 sheet: 3.03 (0.87), residues: 32 loop : -2.87 (0.47), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 315 HIS 0.002 0.001 HIS B 214 PHE 0.015 0.001 PHE B 105 TYR 0.020 0.002 TYR A 241 ARG 0.005 0.000 ARG B 144 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2903.75 seconds wall clock time: 52 minutes 29.99 seconds (3149.99 seconds total)