Starting phenix.real_space_refine on Tue Aug 4 15:08:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ota_70828/08_2026/9ota_70828.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ota_70828/08_2026/9ota_70828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ota_70828/08_2026/9ota_70828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ota_70828/08_2026/9ota_70828.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ota_70828/08_2026/9ota_70828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ota_70828/08_2026/9ota_70828.map" } resolution = 3.2 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= 0.048 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: 6 Type Number sf(0) Gaussians K 4 8.98 5 P 2 5.49 5 S 14 5.16 5 C 2836 2.51 5 N 674 2.21 5 O 726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4256 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2033 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 267, 2017 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 14, 'TRANS': 252} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 267, 2017 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 14, 'TRANS': 252} Chain breaks: 1 bond proxies already assigned to first conformer: 2048 Chain: "A" Number of atoms: 2033 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 267, 2017 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 14, 'TRANS': 252} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 267, 2017 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 14, 'TRANS': 252} Chain breaks: 1 bond proxies already assigned to first conformer: 2048 Chain: "B" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 93 Unusual residues: {'LBN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 10 Chain: "A" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 97 Unusual residues: {' K': 4, 'LBN': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 10 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AGLY B 110 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY B 110 " occ=0.50 residue: pdb=" N ATYR B 111 " occ=0.80 ... (22 atoms not shown) pdb=" OH BTYR B 111 " occ=0.20 residue: pdb=" N AGLY A 110 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 110 " occ=0.50 residue: pdb=" N ATYR A 111 " occ=0.80 ... (22 atoms not shown) pdb=" OH BTYR A 111 " occ=0.20 Time building chain proxies: 2.09, per 1000 atoms: 0.49 Number of scatterers: 4256 At special positions: 0 Unit cell: (65.13, 70.975, 94.355, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 4 19.00 S 14 16.00 P 2 15.00 O 726 8.00 N 674 7.00 C 2836 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS A 53 " 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: 0.47 Conformation dependent library (CDL) restraints added in 379.8 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: 1000 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 78.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'B' and resid 6 through 51 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 55 through 70 Processing helix chain 'B' and resid 72 through 80 removed outlier: 4.028A pdb=" N VAL B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 77 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA B 80 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 105 Processing helix chain 'B' and resid 116 through 150 Proline residue: B 132 - end of helix Processing helix chain 'B' and resid 166 through 185 Processing helix chain 'B' and resid 185 through 196 removed outlier: 3.521A pdb=" N ALA B 189 " --> pdb=" O PHE B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 213 Processing helix chain 'B' and resid 230 through 264 removed outlier: 3.883A pdb=" N HIS B 263 " --> pdb=" O VAL B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 270 Processing helix chain 'A' and resid 6 through 51 Proline residue: A 31 - end of helix removed outlier: 3.616A pdb=" N SER A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 70 Processing helix chain 'A' and resid 70 through 80 removed outlier: 3.921A pdb=" N ARG A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 105 Processing helix chain 'A' and resid 116 through 150 Proline residue: A 132 - end of helix Processing helix chain 'A' and resid 165 through 185 Processing helix chain 'A' and resid 185 through 196 Processing helix chain 'A' and resid 200 through 213 Processing helix chain 'A' and resid 230 through 263 removed outlier: 3.889A pdb=" N HIS A 263 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 270 removed outlier: 3.844A pdb=" N ILE A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) 316 hydrogen bonds defined for protein. 948 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: 0.62 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 718 1.33 - 1.45: 1096 1.45 - 1.57: 2512 1.57 - 1.69: 4 1.69 - 1.82: 20 Bond restraints: 4350 Sorted by residual: bond pdb=" N ARG B 160 " pdb=" CA ARG B 160 " ideal model delta sigma weight residual 1.458 1.475 -0.017 1.90e-02 2.77e+03 8.34e-01 bond pdb=" CB PRO B 52 " pdb=" CG PRO B 52 " ideal model delta sigma weight residual 1.492 1.533 -0.041 5.00e-02 4.00e+02 6.84e-01 bond pdb=" CB BTYR A 111 " pdb=" CG BTYR A 111 " ideal model delta sigma weight residual 1.512 1.527 -0.015 2.20e-02 2.07e+03 4.80e-01 bond pdb=" C VAL A 131 " pdb=" N PRO A 132 " ideal model delta sigma weight residual 1.335 1.344 -0.009 1.36e-02 5.41e+03 3.95e-01 bond pdb=" C VAL B 131 " pdb=" N PRO B 132 " ideal model delta sigma weight residual 1.335 1.343 -0.008 1.36e-02 5.41e+03 3.45e-01 ... (remaining 4345 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 5699 1.07 - 2.15: 157 2.15 - 3.22: 39 3.22 - 4.30: 7 4.30 - 5.37: 10 Bond angle restraints: 5912 Sorted by residual: angle pdb=" C HIS A 263 " pdb=" N GLY A 264 " pdb=" CA GLY A 264 " ideal model delta sigma weight residual 121.41 126.57 -5.16 1.96e+00 2.60e-01 6.94e+00 angle pdb=" N GLY A 130 " pdb=" CA GLY A 130 " pdb=" C GLY A 130 " ideal model delta sigma weight residual 113.18 118.34 -5.16 2.37e+00 1.78e-01 4.74e+00 angle pdb=" N GLY B 130 " pdb=" CA GLY B 130 " pdb=" C GLY B 130 " ideal model delta sigma weight residual 113.18 117.53 -4.35 2.37e+00 1.78e-01 3.37e+00 angle pdb=" C BTYR A 111 " pdb=" N THR A 112 " pdb=" CA THR A 112 " ideal model delta sigma weight residual 122.99 125.53 -2.54 1.41e+00 5.03e-01 3.25e+00 angle pdb=" C GLY A 82 " pdb=" N SER A 83 " pdb=" CA SER A 83 " ideal model delta sigma weight residual 121.54 124.90 -3.36 1.91e+00 2.74e-01 3.09e+00 ... (remaining 5907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.24: 2521 35.24 - 70.48: 60 70.48 - 105.73: 1 105.73 - 140.97: 2 140.97 - 176.21: 1 Dihedral angle restraints: 2585 sinusoidal: 1029 harmonic: 1556 Sorted by residual: dihedral pdb=" C39 LBN A 302 " pdb=" C40 LBN A 302 " pdb=" C41 LBN A 302 " pdb=" C42 LBN A 302 " ideal model delta sinusoidal sigma weight residual 178.66 -5.13 -176.21 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C37 LBN A 302 " pdb=" C38 LBN A 302 " pdb=" C39 LBN A 302 " pdb=" C40 LBN A 302 " ideal model delta sinusoidal sigma weight residual -178.84 -45.75 -133.09 1 3.00e+01 1.11e-03 1.80e+01 dihedral pdb=" O5 LBN B 302 " pdb=" C2 LBN B 302 " pdb=" C3 LBN B 302 " pdb=" O7 LBN B 302 " ideal model delta sinusoidal sigma weight residual 62.67 -66.86 129.53 1 3.00e+01 1.11e-03 1.75e+01 ... (remaining 2582 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 470 0.028 - 0.056: 164 0.056 - 0.084: 44 0.084 - 0.112: 21 0.112 - 0.140: 1 Chirality restraints: 700 Sorted by residual: chirality pdb=" CB VAL A 54 " pdb=" CA VAL A 54 " pdb=" CG1 VAL A 54 " pdb=" CG2 VAL A 54 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA PRO A 31 " pdb=" N PRO A 31 " pdb=" C PRO A 31 " pdb=" CB PRO A 31 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.98e-01 chirality pdb=" CA PRO B 31 " pdb=" N PRO B 31 " pdb=" C PRO B 31 " pdb=" CB PRO B 31 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.98e-01 ... (remaining 697 not shown) Planarity restraints: 720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 271 " -0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO B 272 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 272 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 272 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 160 " 0.135 9.50e-02 1.11e+02 6.05e-02 2.35e+00 pdb=" NE ARG A 160 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARG A 160 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 160 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 160 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 164 " -0.017 5.00e-02 4.00e+02 2.54e-02 1.03e+00 pdb=" N PRO A 165 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 165 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 165 " -0.014 5.00e-02 4.00e+02 ... (remaining 717 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.80: 1005 2.80 - 3.39: 4932 3.39 - 3.97: 7698 3.97 - 4.56: 10870 4.56 - 5.14: 15447 Nonbonded interactions: 39952 Sorted by model distance: nonbonded pdb=" O SER A 146 " pdb=" OG1 THR A 150 " model vdw 2.220 3.040 nonbonded pdb=" O SER B 146 " pdb=" OG1 THR B 150 " model vdw 2.227 3.040 nonbonded pdb=" OG1 THR A 102 " pdb=" OH BTYR A 111 " model vdw 2.324 3.040 nonbonded pdb=" OH TYR B 220 " pdb=" NZ LYS A 120 " model vdw 2.333 3.120 nonbonded pdb=" O SER A 213 " pdb=" OG1 THR A 214 " model vdw 2.409 3.040 ... (remaining 39947 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 4 through 109 or resid 112 through 302)) selection = (chain 'B' and (resid 4 through 109 or resid 112 through 302)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.20 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.610 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 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 : 0.002 0.041 4351 Z= 0.108 Angle : 0.488 5.374 5914 Z= 0.249 Chirality : 0.034 0.140 700 Planarity : 0.004 0.060 720 Dihedral : 15.006 176.210 1582 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.33 % Allowed : 3.12 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.74 (0.39), residues: 534 helix: 3.58 (0.26), residues: 390 sheet: None (None), residues: 0 loop : -0.89 (0.58), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 160 TYR 0.013 0.001 TYR A 206 PHE 0.013 0.001 PHE B 126 TRP 0.005 0.001 TRP A 171 HIS 0.001 0.000 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 ( 4350) covalent geometry : angle 0.48758 / 0.25 ( 5912) SS BOND : bond 0.00040 / 0.03 ( 1) SS BOND : angle 0.63261 / 0.28 ( 2) hydrogen bonds : bond 0.11228 / 7.41 ( 316) hydrogen bonds : angle 4.47810 / 3.36 ( 948) *********************** 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 64 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.090 Fit side-chains revert: symmetry clash REVERT: B 48 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7904 (mm) outliers start: 16 outliers final: 5 residues processed: 60 average time/residue: 0.0911 time to fit residues: 6.6411 Evaluate side-chains 46 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 256 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 0.0970 chunk 30 optimal weight: 1.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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 = 0.4124 r_free = 0.4124 target = 0.190782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.121878 restraints weight = 19127.288| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 4.68 r_work: 0.2840 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.0800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4351 Z= 0.131 Angle : 0.575 16.346 5914 Z= 0.272 Chirality : 0.035 0.175 700 Planarity : 0.004 0.040 720 Dihedral : 15.704 179.454 754 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.64 % Allowed : 6.49 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.69 (0.39), residues: 534 helix: 3.47 (0.26), residues: 404 sheet: None (None), residues: 0 loop : -1.21 (0.61), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 257 TYR 0.013 0.001 TYR B 206 PHE 0.014 0.002 PHE B 126 TRP 0.016 0.001 TRP B 156 HIS 0.002 0.000 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 4350) covalent geometry : angle 0.57429 / 0.27 ( 5912) SS BOND : bond 0.00300 / 0.19 ( 1) SS BOND : angle 1.74508 / 0.81 ( 2) hydrogen bonds : bond 0.03975 / 2.70 ( 316) hydrogen bonds : angle 3.47441 / 2.58 ( 948) *********************** 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 49 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.085 Fit side-chains revert: symmetry clash REVERT: B 24 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8185 (tt) REVERT: B 48 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7643 (mm) REVERT: B 166 ARG cc_start: 0.5530 (mmm160) cc_final: 0.5258 (mmm160) REVERT: A 33 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8319 (tt0) outliers start: 9 outliers final: 5 residues processed: 48 average time/residue: 0.0630 time to fit residues: 3.6974 Evaluate side-chains 46 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 256 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.4090 r_free = 0.4090 target = 0.186081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.123659 restraints weight = 15461.878| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 5.09 r_work: 0.2922 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4351 Z= 0.174 Angle : 0.572 11.251 5914 Z= 0.284 Chirality : 0.036 0.151 700 Planarity : 0.004 0.038 720 Dihedral : 15.380 177.985 754 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.37 % Allowed : 8.17 % Favored : 88.46 % 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: 3.54 (0.39), residues: 534 helix: 3.38 (0.25), residues: 404 sheet: None (None), residues: 0 loop : -1.32 (0.61), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 50 TYR 0.017 0.002 TYR B 206 PHE 0.020 0.002 PHE A 126 TRP 0.006 0.001 TRP A 91 HIS 0.001 0.000 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.17 ( 4350) covalent geometry : angle 0.57152 / 0.28 ( 5912) SS BOND : bond 0.00232 / 0.14 ( 1) SS BOND : angle 1.52052 / 0.67 ( 2) hydrogen bonds : bond 0.04517 / 3.07 ( 316) hydrogen bonds : angle 3.45360 / 2.57 ( 948) *********************** 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 52 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: B 24 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8392 (tt) REVERT: B 48 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7914 (mm) REVERT: B 166 ARG cc_start: 0.5626 (mmm160) cc_final: 0.4819 (mmm160) outliers start: 12 outliers final: 8 residues processed: 51 average time/residue: 0.0914 time to fit residues: 5.7909 Evaluate side-chains 49 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 256 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 3 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 6 optimal weight: 0.0070 chunk 37 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- 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 = 0.4112 r_free = 0.4112 target = 0.188936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.128156 restraints weight = 15523.547| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 5.30 r_work: 0.2797 rms_B_bonded: 5.09 restraints_weight: 2.0000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (14 function evaluations) r_final: 0.2905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4351 Z= 0.122 Angle : 0.555 10.771 5914 Z= 0.266 Chirality : 0.034 0.138 700 Planarity : 0.004 0.047 720 Dihedral : 14.844 168.563 754 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.64 % Allowed : 9.38 % Favored : 87.98 % 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: 3.67 (0.39), residues: 534 helix: 3.49 (0.25), residues: 404 sheet: None (None), residues: 0 loop : -1.34 (0.60), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 74 TYR 0.012 0.001 TYR B 206 PHE 0.013 0.001 PHE B 126 TRP 0.003 0.001 TRP A 171 HIS 0.001 0.000 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 4350) covalent geometry : angle 0.55387 / 0.27 ( 5912) SS BOND : bond 0.00297 / 0.19 ( 1) SS BOND : angle 1.58325 / 0.69 ( 2) hydrogen bonds : bond 0.03823 / 2.59 ( 316) hydrogen bonds : angle 3.29596 / 2.44 ( 948) *********************** 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 53 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.086 Fit side-chains revert: symmetry clash REVERT: B 24 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8363 (tt) REVERT: B 48 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7895 (mm) REVERT: B 166 ARG cc_start: 0.5547 (mmm160) cc_final: 0.4808 (mmm160) REVERT: B 249 MET cc_start: 0.8761 (mmp) cc_final: 0.8555 (mmp) outliers start: 9 outliers final: 6 residues processed: 52 average time/residue: 0.0636 time to fit residues: 4.1404 Evaluate side-chains 51 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 259 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 19 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 0.2980 chunk 18 optimal weight: 0.0020 chunk 43 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.5990 ------------------------------------------------------------------------------- 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 = 0.4121 r_free = 0.4121 target = 0.189803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.129576 restraints weight = 15500.425| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 5.24 r_work: 0.2818 rms_B_bonded: 5.12 restraints_weight: 2.0000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4351 Z= 0.115 Angle : 0.534 10.080 5914 Z= 0.259 Chirality : 0.034 0.134 700 Planarity : 0.004 0.052 720 Dihedral : 14.278 154.074 754 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.88 % Allowed : 9.38 % Favored : 87.74 % 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: 3.68 (0.39), residues: 534 helix: 3.51 (0.25), residues: 404 sheet: None (None), residues: 0 loop : -1.40 (0.60), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 74 TYR 0.011 0.001 TYR B 17 PHE 0.012 0.001 PHE B 126 TRP 0.005 0.001 TRP B 91 HIS 0.001 0.000 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 4350) covalent geometry : angle 0.53317 / 0.26 ( 5912) SS BOND : bond 0.00281 / 0.18 ( 1) SS BOND : angle 1.50215 / 0.64 ( 2) hydrogen bonds : bond 0.03608 / 2.45 ( 316) hydrogen bonds : angle 3.20042 / 2.36 ( 948) *********************** 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 57 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: B 24 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8356 (tt) REVERT: B 48 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7914 (mm) REVERT: B 166 ARG cc_start: 0.5679 (mmm160) cc_final: 0.4995 (mmm160) REVERT: A 224 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8805 (mm-30) outliers start: 10 outliers final: 7 residues processed: 54 average time/residue: 0.0547 time to fit residues: 3.7277 Evaluate side-chains 56 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 256 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 14 optimal weight: 0.4980 chunk 22 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 15 optimal weight: 10.0000 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 = 0.4114 r_free = 0.4114 target = 0.189037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.125524 restraints weight = 14097.098| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 4.95 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.3264 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4351 Z= 0.124 Angle : 0.559 11.595 5914 Z= 0.268 Chirality : 0.034 0.132 700 Planarity : 0.004 0.056 720 Dihedral : 14.021 147.119 754 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.88 % Allowed : 9.62 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.67 (0.39), residues: 534 helix: 3.51 (0.25), residues: 404 sheet: None (None), residues: 0 loop : -1.42 (0.60), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 74 TYR 0.011 0.001 TYR B 17 PHE 0.012 0.002 PHE B 126 TRP 0.006 0.001 TRP B 91 HIS 0.001 0.000 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 ( 4350) covalent geometry : angle 0.55858 / 0.27 ( 5912) SS BOND : bond 0.00263 / 0.16 ( 1) SS BOND : angle 1.51555 / 0.64 ( 2) hydrogen bonds : bond 0.03667 / 2.49 ( 316) hydrogen bonds : angle 3.19723 / 2.36 ( 948) *********************** 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 56 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: B 24 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8086 (tt) REVERT: A 224 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8705 (mm-30) outliers start: 10 outliers final: 8 residues processed: 53 average time/residue: 0.0851 time to fit residues: 5.6326 Evaluate side-chains 55 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 259 VAL 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 24 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4113 r_free = 0.4113 target = 0.188770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.125216 restraints weight = 20654.238| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 5.11 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3044 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4351 Z= 0.124 Angle : 0.550 9.617 5914 Z= 0.267 Chirality : 0.034 0.133 700 Planarity : 0.004 0.058 720 Dihedral : 13.722 140.940 752 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.88 % Allowed : 8.41 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.68 (0.39), residues: 534 helix: 3.47 (0.25), residues: 406 sheet: None (None), residues: 0 loop : -1.30 (0.60), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 74 TYR 0.011 0.001 TYR B 17 PHE 0.012 0.002 PHE B 126 TRP 0.004 0.001 TRP B 91 HIS 0.002 0.000 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 ( 4350) covalent geometry : angle 0.54944 / 0.27 ( 5912) SS BOND : bond 0.00266 / 0.17 ( 1) SS BOND : angle 1.49291 / 0.64 ( 2) hydrogen bonds : bond 0.03681 / 2.50 ( 316) hydrogen bonds : angle 3.19207 / 2.36 ( 948) *********************** 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 59 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.086 Fit side-chains revert: symmetry clash REVERT: B 24 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8075 (tt) REVERT: B 48 LEU cc_start: 0.8003 (mm) cc_final: 0.7778 (mm) REVERT: B 166 ARG cc_start: 0.5503 (mmm160) cc_final: 0.4742 (mmm160) REVERT: A 224 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8759 (mm-30) outliers start: 10 outliers final: 8 residues processed: 55 average time/residue: 0.0530 time to fit residues: 3.7102 Evaluate side-chains 58 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 259 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 3 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 0.0370 chunk 7 optimal weight: 5.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- 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 = 0.4115 r_free = 0.4115 target = 0.188869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.129040 restraints weight = 18132.274| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 5.52 r_work: 0.2664 rms_B_bonded: 5.27 restraints_weight: 2.0000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.2833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4351 Z= 0.121 Angle : 0.534 9.558 5914 Z= 0.261 Chirality : 0.034 0.129 700 Planarity : 0.004 0.057 720 Dihedral : 13.446 131.529 752 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.88 % Allowed : 8.41 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.70 (0.39), residues: 534 helix: 3.53 (0.25), residues: 404 sheet: None (None), residues: 0 loop : -1.41 (0.60), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 74 TYR 0.011 0.001 TYR B 17 PHE 0.012 0.002 PHE B 126 TRP 0.004 0.001 TRP B 91 HIS 0.002 0.000 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 4350) covalent geometry : angle 0.53340 / 0.26 ( 5912) SS BOND : bond 0.00248 / 0.16 ( 1) SS BOND : angle 1.49782 / 0.64 ( 2) hydrogen bonds : bond 0.03636 / 2.47 ( 316) hydrogen bonds : angle 3.16259 / 2.33 ( 948) *********************** 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 58 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: B 24 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8150 (tt) REVERT: B 29 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7935 (mm-30) REVERT: B 50 ARG cc_start: 0.7993 (tpp80) cc_final: 0.7609 (ttp80) REVERT: B 166 ARG cc_start: 0.5329 (mmm160) cc_final: 0.4367 (mmm160) outliers start: 10 outliers final: 9 residues processed: 55 average time/residue: 0.0937 time to fit residues: 6.3087 Evaluate side-chains 57 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 259 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 22 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 14 optimal weight: 0.1980 chunk 38 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4110 r_free = 0.4110 target = 0.188443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.120644 restraints weight = 20607.189| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 5.00 r_work: 0.2655 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (14 function evaluations) r_final: 0.2850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4351 Z= 0.124 Angle : 0.547 9.384 5914 Z= 0.265 Chirality : 0.034 0.131 700 Planarity : 0.004 0.062 720 Dihedral : 13.323 124.577 752 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.40 % Allowed : 9.13 % Favored : 88.46 % 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: 3.70 (0.39), residues: 534 helix: 3.48 (0.25), residues: 406 sheet: None (None), residues: 0 loop : -1.30 (0.61), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 74 TYR 0.011 0.001 TYR A 17 PHE 0.012 0.002 PHE B 126 TRP 0.004 0.000 TRP B 91 HIS 0.002 0.000 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 ( 4350) covalent geometry : angle 0.54637 / 0.26 ( 5912) SS BOND : bond 0.00223 / 0.14 ( 1) SS BOND : angle 1.48057 / 0.63 ( 2) hydrogen bonds : bond 0.03664 / 2.49 ( 316) hydrogen bonds : angle 3.16198 / 2.34 ( 948) *********************** 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 55 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.101 Fit side-chains revert: symmetry clash REVERT: B 24 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8055 (tt) REVERT: B 50 ARG cc_start: 0.7949 (tpp80) cc_final: 0.7569 (ttp80) REVERT: B 166 ARG cc_start: 0.5312 (mmm160) cc_final: 0.4392 (mmm160) outliers start: 8 outliers final: 7 residues processed: 53 average time/residue: 0.0819 time to fit residues: 5.2224 Evaluate side-chains 55 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 256 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 48 optimal weight: 0.2980 chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4115 r_free = 0.4115 target = 0.188884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.119456 restraints weight = 20294.583| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 4.67 r_work: 0.2712 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (11 function evaluations) r_final: 0.2883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4351 Z= 0.120 Angle : 0.535 9.392 5914 Z= 0.261 Chirality : 0.034 0.128 700 Planarity : 0.004 0.061 720 Dihedral : 13.023 114.561 752 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.64 % Allowed : 8.89 % Favored : 88.46 % 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: 3.71 (0.39), residues: 534 helix: 3.49 (0.25), residues: 406 sheet: None (None), residues: 0 loop : -1.29 (0.61), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 74 TYR 0.011 0.001 TYR B 17 PHE 0.011 0.001 PHE B 126 TRP 0.004 0.000 TRP B 91 HIS 0.003 0.000 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 4350) covalent geometry : angle 0.53470 / 0.26 ( 5912) SS BOND : bond 0.00222 / 0.14 ( 1) SS BOND : angle 1.45424 / 0.61 ( 2) hydrogen bonds : bond 0.03592 / 2.44 ( 316) hydrogen bonds : angle 3.14160 / 2.32 ( 948) ********************** 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 57 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.148 Fit side-chains revert: symmetry clash REVERT: B 24 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8120 (tt) REVERT: B 50 ARG cc_start: 0.7987 (tpp80) cc_final: 0.7616 (ttp80) REVERT: B 166 ARG cc_start: 0.5345 (mmm160) cc_final: 0.4450 (mmm160) outliers start: 9 outliers final: 8 residues processed: 55 average time/residue: 0.0924 time to fit residues: 6.2771 Evaluate side-chains 56 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 256 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 4 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 chunk 26 optimal weight: 0.2980 chunk 9 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4118 r_free = 0.4118 target = 0.189147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.119996 restraints weight = 18139.980| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 4.24 r_work: 0.2688 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (7 function evaluations) r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4351 Z= 0.118 Angle : 0.541 9.293 5914 Z= 0.262 Chirality : 0.034 0.128 700 Planarity : 0.004 0.062 720 Dihedral : 12.652 114.205 752 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.64 % Allowed : 8.89 % Favored : 88.46 % 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: 3.73 (0.39), residues: 534 helix: 3.51 (0.25), residues: 406 sheet: None (None), residues: 0 loop : -1.29 (0.61), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 74 TYR 0.011 0.001 TYR A 17 PHE 0.011 0.001 PHE B 126 TRP 0.004 0.001 TRP B 91 HIS 0.002 0.000 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 4350) covalent geometry : angle 0.54072 / 0.26 ( 5912) SS BOND : bond 0.00233 / 0.15 ( 1) SS BOND : angle 1.42881 / 0.60 ( 2) hydrogen bonds : bond 0.03560 / 2.42 ( 316) hydrogen bonds : angle 3.12652 / 2.31 ( 948) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1218.97 seconds wall clock time: 21 minutes 27.77 seconds (1287.77 seconds total)