Starting phenix.real_space_refine on Thu Mar 6 08:15:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ivk_60929/03_2025/9ivk_60929_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ivk_60929/03_2025/9ivk_60929.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ivk_60929/03_2025/9ivk_60929.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ivk_60929/03_2025/9ivk_60929.map" model { file = "/net/cci-nas-00/data/ceres_data/9ivk_60929/03_2025/9ivk_60929_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ivk_60929/03_2025/9ivk_60929_neut.cif" } resolution = 2.74 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= 0.000 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1806 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 2640 2.51 5 N 654 2.21 5 O 769 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4077 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2271 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 3, 'TRANS': 274} Chain breaks: 1 Chain: "H" Number of atoms: 958 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 122, 943 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 117} Conformer: "B" Number of residues, atoms: 122, 943 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 117} bond proxies already assigned to first conformer: 953 Chain: "L" Number of atoms: 822 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 107, 819 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Conformer: "B" Number of residues, atoms: 107, 819 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} bond proxies already assigned to first conformer: 833 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'KY6': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.81, per 1000 atoms: 0.93 Number of scatterers: 4077 At special positions: 0 Unit cell: (54.72, 72.96, 143.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 769 8.00 N 654 7.00 C 2640 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG ACYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG BCYS H 99 " distance=2.03 Simple disulfide: pdb=" SG ACYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS L 89 " - pdb=" SG BCYS L 24 " 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: 1.04 Conformation dependent library (CDL) restraints added in 676.4 milliseconds 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 968 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 6 sheets defined 56.4% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 1 through 36 removed outlier: 4.467A pdb=" N LYS A 36 " --> pdb=" O GLU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 48 Processing helix chain 'A' and resid 48 through 110 Processing helix chain 'A' and resid 112 through 133 removed outlier: 3.567A pdb=" N VAL A 116 " --> pdb=" O ASN A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 171 removed outlier: 3.572A pdb=" N GLU A 171 " --> pdb=" O LYS A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 192 Processing helix chain 'A' and resid 192 through 243 Processing helix chain 'A' and resid 248 through 285 Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.866A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 112 Processing helix chain 'L' and resid 94 through 98 removed outlier: 4.100A pdb=" N VAL L 98 " --> pdb=" O TYR L 95 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA2, first strand: chain 'H' and resid 60 through 63 removed outlier: 6.571A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR H 53 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU H 37 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N SER H 55 " --> pdb=" O PHE H 35 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N PHE H 35 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TYR H 116 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 60 through 63 removed outlier: 6.571A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR H 53 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU H 37 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N SER H 55 " --> pdb=" O PHE H 35 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N PHE H 35 " --> pdb=" O SER H 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AA5, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.858A pdb=" N LEU L 12 " --> pdb=" O GLU L 107 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.858A pdb=" N LEU L 12 " --> pdb=" O GLU L 107 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR L 99 " --> pdb=" O GLN L 91 " (cutoff:3.500A) 325 hydrogen bonds defined for protein. 923 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: 1.16 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 681 1.28 - 1.41: 1010 1.41 - 1.55: 2446 1.55 - 1.68: 3 1.68 - 1.81: 22 Bond restraints: 4162 Sorted by residual: bond pdb=" C ILE A 50 " pdb=" O ILE A 50 " ideal model delta sigma weight residual 1.236 1.283 -0.047 1.23e-02 6.61e+03 1.46e+01 bond pdb=" N ILE A 48 " pdb=" CA ILE A 48 " ideal model delta sigma weight residual 1.456 1.491 -0.034 9.50e-03 1.11e+04 1.31e+01 bond pdb=" N ILE A 241 " pdb=" CA ILE A 241 " ideal model delta sigma weight residual 1.452 1.494 -0.041 1.18e-02 7.18e+03 1.24e+01 bond pdb=" N ILE A 8 " pdb=" CA ILE A 8 " ideal model delta sigma weight residual 1.462 1.499 -0.037 1.18e-02 7.18e+03 1.01e+01 bond pdb=" N LYS A 239 " pdb=" CA LYS A 239 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.33e-02 5.65e+03 9.97e+00 ... (remaining 4157 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 5441 2.39 - 4.78: 173 4.78 - 7.17: 13 7.17 - 9.56: 0 9.56 - 11.95: 3 Bond angle restraints: 5630 Sorted by residual: angle pdb=" N LYS A 49 " pdb=" CA LYS A 49 " pdb=" C LYS A 49 " ideal model delta sigma weight residual 113.19 101.24 11.95 1.19e+00 7.06e-01 1.01e+02 angle pdb=" N ILE A 48 " pdb=" CA ILE A 48 " pdb=" C ILE A 48 " ideal model delta sigma weight residual 113.53 103.86 9.67 9.80e-01 1.04e+00 9.74e+01 angle pdb=" N LYS A 240 " pdb=" CA LYS A 240 " pdb=" C LYS A 240 " ideal model delta sigma weight residual 113.01 102.76 10.25 1.20e+00 6.94e-01 7.29e+01 angle pdb=" N PHE A 10 " pdb=" CA PHE A 10 " pdb=" C PHE A 10 " ideal model delta sigma weight residual 111.36 105.57 5.79 1.09e+00 8.42e-01 2.82e+01 angle pdb=" CA THR A 238 " pdb=" C THR A 238 " pdb=" O THR A 238 " ideal model delta sigma weight residual 120.82 115.70 5.12 1.05e+00 9.07e-01 2.38e+01 ... (remaining 5625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 2249 17.53 - 35.06: 209 35.06 - 52.59: 34 52.59 - 70.13: 9 70.13 - 87.66: 12 Dihedral angle restraints: 2513 sinusoidal: 1011 harmonic: 1502 Sorted by residual: dihedral pdb=" CB ACYS L 24 " pdb=" SG ACYS L 24 " pdb=" SG CYS L 89 " pdb=" CB CYS L 89 " ideal model delta sinusoidal sigma weight residual 93.00 56.56 36.44 1 1.00e+01 1.00e-02 1.88e+01 dihedral pdb=" C LYS A 239 " pdb=" N LYS A 239 " pdb=" CA LYS A 239 " pdb=" CB LYS A 239 " ideal model delta harmonic sigma weight residual -122.60 -131.80 9.20 0 2.50e+00 1.60e-01 1.35e+01 dihedral pdb=" CB CYS H 25 " pdb=" SG CYS H 25 " pdb=" SG ACYS H 99 " pdb=" CB ACYS H 99 " ideal model delta sinusoidal sigma weight residual 93.00 63.37 29.63 1 1.00e+01 1.00e-02 1.25e+01 ... (remaining 2510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 510 0.060 - 0.120: 84 0.120 - 0.180: 26 0.180 - 0.240: 8 0.240 - 0.299: 5 Chirality restraints: 633 Sorted by residual: chirality pdb=" CA LYS A 239 " pdb=" N LYS A 239 " pdb=" C LYS A 239 " pdb=" CB LYS A 239 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA ILE A 50 " pdb=" N ILE A 50 " pdb=" C ILE A 50 " pdb=" CB ILE A 50 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA LYS A 49 " pdb=" N LYS A 49 " pdb=" C LYS A 49 " pdb=" CB LYS A 49 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 630 not shown) Planarity restraints: 703 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 242 " -0.021 2.00e-02 2.50e+03 4.39e-02 1.92e+01 pdb=" C LYS A 242 " 0.076 2.00e-02 2.50e+03 pdb=" O LYS A 242 " -0.028 2.00e-02 2.50e+03 pdb=" N GLU A 243 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 236 " -0.014 2.00e-02 2.50e+03 2.91e-02 8.44e+00 pdb=" C PHE A 236 " 0.050 2.00e-02 2.50e+03 pdb=" O PHE A 236 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU A 237 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 9 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.36e+00 pdb=" C LEU A 9 " -0.050 2.00e-02 2.50e+03 pdb=" O LEU A 9 " 0.019 2.00e-02 2.50e+03 pdb=" N PHE A 10 " 0.017 2.00e-02 2.50e+03 ... (remaining 700 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 649 2.76 - 3.30: 3955 3.30 - 3.83: 6991 3.83 - 4.37: 8130 4.37 - 4.90: 13792 Nonbonded interactions: 33517 Sorted by model distance: nonbonded pdb=" OD1 ASP H 76 " pdb=" OG SER H 78 " model vdw 2.231 3.040 nonbonded pdb=" NZ LYS A 41 " pdb=" OD1 ASN A 245 " model vdw 2.253 3.120 nonbonded pdb=" NE2 GLN L 91 " pdb=" O LEU L 97 " model vdw 2.288 3.120 nonbonded pdb=" NH1 ARG L 25 " pdb=" OD2 ASP L 71 " model vdw 2.288 3.120 nonbonded pdb=" OE2 GLU A 212 " pdb=" NZ LYS A 279 " model vdw 2.289 3.120 ... (remaining 33512 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.430 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:12.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 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 : 0.006 0.047 4162 Z= 0.359 Angle : 0.860 11.946 5630 Z= 0.622 Chirality : 0.060 0.299 633 Planarity : 0.005 0.044 703 Dihedral : 14.935 87.656 1533 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.69 % Allowed : 3.67 % Favored : 95.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.92 (0.38), residues: 504 helix: 2.40 (0.31), residues: 258 sheet: -0.11 (0.50), residues: 109 loop : 0.38 (0.57), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 97 HIS 0.001 0.001 HIS H 38 PHE 0.019 0.002 PHE A 151 TYR 0.026 0.001 TYR A 260 ARG 0.002 0.000 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 94 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: A 6 LYS cc_start: 0.7253 (tppp) cc_final: 0.6452 (tmmt) REVERT: A 118 ASP cc_start: 0.7385 (m-30) cc_final: 0.7040 (m-30) REVERT: H 72 THR cc_start: 0.8438 (m) cc_final: 0.8232 (m) REVERT: H 85 GLN cc_start: 0.7999 (tp40) cc_final: 0.7499 (tp40) outliers start: 3 outliers final: 1 residues processed: 96 average time/residue: 1.0172 time to fit residues: 101.4403 Evaluate side-chains 69 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 28 optimal weight: 0.4980 chunk 44 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.4066 r_free = 0.4066 target = 0.175777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.116755 restraints weight = 16759.126| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 5.43 r_work: 0.3018 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 4162 Z= 0.315 Angle : 0.587 6.326 5630 Z= 0.310 Chirality : 0.040 0.139 633 Planarity : 0.004 0.040 703 Dihedral : 4.770 43.091 565 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.75 % Allowed : 15.14 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 2.50 (0.37), residues: 504 helix: 2.96 (0.29), residues: 263 sheet: 0.01 (0.50), residues: 103 loop : 0.49 (0.54), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 97 HIS 0.002 0.001 HIS H 38 PHE 0.039 0.002 PHE L 84 TYR 0.013 0.001 TYR L 92 ARG 0.002 0.000 ARG H 70 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 6 LYS cc_start: 0.7314 (tppp) cc_final: 0.6476 (tmmt) REVERT: A 97 TRP cc_start: 0.7947 (t-100) cc_final: 0.7050 (t-100) REVERT: A 118 ASP cc_start: 0.7922 (m-30) cc_final: 0.7637 (m-30) REVERT: A 194 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7636 (mttt) REVERT: H 85 GLN cc_start: 0.8090 (tp40) cc_final: 0.7709 (tp40) outliers start: 12 outliers final: 6 residues processed: 77 average time/residue: 1.0389 time to fit residues: 83.2263 Evaluate side-chains 75 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain H residue 57 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 32 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4062 r_free = 0.4062 target = 0.175336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.116292 restraints weight = 17156.069| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 5.41 r_work: 0.3019 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 4162 Z= 0.315 Angle : 0.587 6.326 5630 Z= 0.310 Chirality : 0.040 0.139 633 Planarity : 0.004 0.040 703 Dihedral : 4.713 43.091 563 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.61 % Allowed : 17.66 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 2.50 (0.37), residues: 504 helix: 2.96 (0.29), residues: 263 sheet: 0.01 (0.50), residues: 103 loop : 0.49 (0.54), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 97 HIS 0.002 0.001 HIS H 38 PHE 0.039 0.002 PHE L 84 TYR 0.013 0.001 TYR L 92 ARG 0.002 0.000 ARG H 70 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: A 6 LYS cc_start: 0.7324 (tppp) cc_final: 0.6492 (tmmt) REVERT: A 97 TRP cc_start: 0.7962 (t-100) cc_final: 0.7074 (t-100) REVERT: A 118 ASP cc_start: 0.7938 (m-30) cc_final: 0.7656 (m-30) REVERT: A 194 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7655 (mttt) REVERT: H 85 GLN cc_start: 0.8091 (tp40) cc_final: 0.7757 (tp40) outliers start: 7 outliers final: 6 residues processed: 70 average time/residue: 0.9968 time to fit residues: 72.7956 Evaluate side-chains 74 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain H residue 57 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 45 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 11 optimal weight: 0.2980 chunk 12 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4098 r_free = 0.4098 target = 0.179816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.120476 restraints weight = 15678.326| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 4.36 r_work: 0.3161 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4162 Z= 0.197 Angle : 0.502 6.586 5630 Z= 0.268 Chirality : 0.037 0.128 633 Planarity : 0.004 0.038 703 Dihedral : 4.585 39.606 563 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.29 % Allowed : 18.12 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 2.86 (0.37), residues: 504 helix: 3.46 (0.29), residues: 257 sheet: -0.01 (0.51), residues: 106 loop : 0.48 (0.55), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 50 HIS 0.001 0.001 HIS H 38 PHE 0.049 0.002 PHE L 84 TYR 0.011 0.001 TYR L 92 ARG 0.002 0.000 ARG H 90 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: A 6 LYS cc_start: 0.7098 (tppp) cc_final: 0.6232 (tmmt) REVERT: A 118 ASP cc_start: 0.7572 (m-30) cc_final: 0.7314 (m-30) REVERT: A 194 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7382 (mttt) REVERT: H 85 GLN cc_start: 0.7839 (tp40) cc_final: 0.7319 (tp40) REVERT: L 4 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.8016 (mp-120) REVERT: L 71 ASP cc_start: 0.8266 (m-30) cc_final: 0.8003 (m-30) outliers start: 10 outliers final: 4 residues processed: 75 average time/residue: 0.9974 time to fit residues: 77.8852 Evaluate side-chains 78 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain L residue 4 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.0980 chunk 35 optimal weight: 9.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.177505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.117112 restraints weight = 16918.871| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 4.49 r_work: 0.3139 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 4162 Z= 0.373 Angle : 0.575 7.671 5630 Z= 0.300 Chirality : 0.040 0.149 633 Planarity : 0.004 0.043 703 Dihedral : 4.627 39.529 563 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.21 % Allowed : 18.12 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 2.71 (0.38), residues: 504 helix: 3.23 (0.29), residues: 263 sheet: -0.13 (0.51), residues: 106 loop : 0.57 (0.58), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 97 HIS 0.002 0.001 HIS H 38 PHE 0.048 0.002 PHE L 84 TYR 0.011 0.002 TYR L 50 ARG 0.006 0.001 ARG L 25 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 6 LYS cc_start: 0.7155 (tppp) cc_final: 0.6291 (tmmt) REVERT: A 118 ASP cc_start: 0.7692 (m-30) cc_final: 0.7437 (m-30) REVERT: A 194 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7485 (mttt) REVERT: H 53 TYR cc_start: 0.9352 (OUTLIER) cc_final: 0.9077 (p90) REVERT: H 63 TYR cc_start: 0.9020 (m-80) cc_final: 0.8807 (m-80) REVERT: H 85 GLN cc_start: 0.7929 (tp40) cc_final: 0.7516 (tp40) REVERT: L 82 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7883 (pm20) outliers start: 14 outliers final: 7 residues processed: 76 average time/residue: 0.8875 time to fit residues: 70.5382 Evaluate side-chains 73 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain L residue 82 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 1 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 0 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.4090 r_free = 0.4090 target = 0.178517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.119092 restraints weight = 17976.872| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 5.00 r_work: 0.3126 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3114 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 4162 Z= 0.373 Angle : 0.575 7.670 5630 Z= 0.300 Chirality : 0.040 0.149 633 Planarity : 0.004 0.043 703 Dihedral : 4.650 39.529 563 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.29 % Allowed : 19.50 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 2.71 (0.38), residues: 504 helix: 3.23 (0.29), residues: 263 sheet: -0.13 (0.51), residues: 106 loop : 0.57 (0.58), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 97 HIS 0.002 0.001 HIS H 38 PHE 0.048 0.002 PHE L 84 TYR 0.011 0.002 TYR L 50 ARG 0.006 0.001 ARG L 25 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 6 LYS cc_start: 0.7105 (tppp) cc_final: 0.6242 (tmmt) REVERT: A 118 ASP cc_start: 0.7551 (m-30) cc_final: 0.7286 (m-30) REVERT: A 194 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7409 (mttt) REVERT: H 53 TYR cc_start: 0.9313 (OUTLIER) cc_final: 0.9034 (p90) REVERT: H 63 TYR cc_start: 0.8982 (m-80) cc_final: 0.8757 (m-80) REVERT: H 85 GLN cc_start: 0.7827 (tp40) cc_final: 0.7420 (tp40) REVERT: L 82 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7847 (pm20) outliers start: 10 outliers final: 7 residues processed: 68 average time/residue: 0.9990 time to fit residues: 70.8753 Evaluate side-chains 73 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain L residue 82 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 33 optimal weight: 0.0040 chunk 3 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 overall best weight: 0.6592 ------------------------------------------------------------------------------- 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 = 0.4070 r_free = 0.4070 target = 0.177130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.118616 restraints weight = 12547.985| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 3.89 r_work: 0.3151 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 4162 Z= 0.370 Angle : 0.574 7.658 5630 Z= 0.300 Chirality : 0.040 0.147 633 Planarity : 0.004 0.043 703 Dihedral : 4.790 39.532 563 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.29 % Allowed : 19.50 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 2.71 (0.38), residues: 504 helix: 3.23 (0.29), residues: 263 sheet: -0.13 (0.51), residues: 106 loop : 0.57 (0.58), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 97 HIS 0.002 0.001 HIS H 38 PHE 0.047 0.002 PHE L 84 TYR 0.011 0.002 TYR L 50 ARG 0.006 0.001 ARG L 25 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 6 LYS cc_start: 0.7159 (tppp) cc_final: 0.6303 (tmmt) REVERT: A 118 ASP cc_start: 0.7671 (m-30) cc_final: 0.7413 (m-30) REVERT: A 194 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7482 (mttt) REVERT: H 53 TYR cc_start: 0.9347 (OUTLIER) cc_final: 0.9075 (p90) REVERT: H 63 TYR cc_start: 0.9021 (m-80) cc_final: 0.8806 (m-80) REVERT: H 85 GLN cc_start: 0.7932 (tp40) cc_final: 0.7518 (tp40) REVERT: L 82 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7874 (pm20) outliers start: 10 outliers final: 7 residues processed: 68 average time/residue: 0.9734 time to fit residues: 69.1098 Evaluate side-chains 73 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain L residue 82 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 46 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.179701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.118180 restraints weight = 22799.000| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 5.50 r_work: 0.3135 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4162 Z= 0.241 Angle : 0.550 9.376 5630 Z= 0.285 Chirality : 0.038 0.135 633 Planarity : 0.004 0.041 703 Dihedral : 4.645 39.453 563 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.29 % Allowed : 19.50 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 2.79 (0.38), residues: 504 helix: 3.27 (0.29), residues: 263 sheet: 0.02 (0.51), residues: 103 loop : 0.52 (0.57), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 97 HIS 0.002 0.001 HIS H 38 PHE 0.053 0.002 PHE L 84 TYR 0.011 0.001 TYR L 92 ARG 0.006 0.001 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 6 LYS cc_start: 0.7106 (tppp) cc_final: 0.6233 (tmmt) REVERT: A 118 ASP cc_start: 0.7525 (m-30) cc_final: 0.7265 (m-30) REVERT: A 194 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7399 (mttt) REVERT: H 53 TYR cc_start: 0.9283 (OUTLIER) cc_final: 0.9014 (p90) REVERT: H 85 GLN cc_start: 0.7842 (tp40) cc_final: 0.7429 (tp40) REVERT: L 82 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7837 (pm20) outliers start: 10 outliers final: 6 residues processed: 68 average time/residue: 0.9926 time to fit residues: 70.3617 Evaluate side-chains 76 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain L residue 82 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 3 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4081 r_free = 0.4081 target = 0.178321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.119852 restraints weight = 12190.619| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 3.99 r_work: 0.3145 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4162 Z= 0.240 Angle : 0.548 9.325 5630 Z= 0.284 Chirality : 0.038 0.134 633 Planarity : 0.004 0.041 703 Dihedral : 4.666 39.456 563 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.06 % Allowed : 19.50 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 2.79 (0.38), residues: 504 helix: 3.27 (0.29), residues: 263 sheet: 0.02 (0.51), residues: 103 loop : 0.53 (0.57), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 97 HIS 0.002 0.001 HIS H 38 PHE 0.052 0.002 PHE L 84 TYR 0.011 0.001 TYR L 92 ARG 0.006 0.001 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: A 6 LYS cc_start: 0.7154 (tppp) cc_final: 0.6296 (tmmt) REVERT: A 118 ASP cc_start: 0.7671 (m-30) cc_final: 0.7422 (m-30) REVERT: A 194 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7468 (mttt) REVERT: H 53 TYR cc_start: 0.9325 (OUTLIER) cc_final: 0.9062 (p90) REVERT: H 85 GLN cc_start: 0.7942 (tp40) cc_final: 0.7522 (tp40) REVERT: L 82 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7872 (pm20) outliers start: 9 outliers final: 6 residues processed: 71 average time/residue: 0.9980 time to fit residues: 73.9037 Evaluate side-chains 76 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain L residue 82 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 4 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 47 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4106 r_free = 0.4106 target = 0.180234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.120530 restraints weight = 15480.004| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 4.40 r_work: 0.3140 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4162 Z= 0.225 Angle : 0.536 9.501 5630 Z= 0.279 Chirality : 0.037 0.131 633 Planarity : 0.004 0.039 703 Dihedral : 4.624 39.059 563 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.61 % Allowed : 19.95 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 2.80 (0.38), residues: 504 helix: 3.44 (0.28), residues: 257 sheet: -0.11 (0.51), residues: 106 loop : 0.45 (0.56), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 97 HIS 0.002 0.001 HIS H 38 PHE 0.051 0.002 PHE L 84 TYR 0.011 0.001 TYR L 92 ARG 0.002 0.000 ARG L 25 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 6 LYS cc_start: 0.7091 (tppp) cc_final: 0.6203 (tmmt) REVERT: A 194 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7422 (mttt) REVERT: H 53 TYR cc_start: 0.9305 (OUTLIER) cc_final: 0.9044 (p90) REVERT: H 85 GLN cc_start: 0.7879 (tp40) cc_final: 0.7486 (tp40) REVERT: L 82 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7862 (pm20) outliers start: 7 outliers final: 4 residues processed: 70 average time/residue: 1.0061 time to fit residues: 73.5298 Evaluate side-chains 70 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain L residue 82 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 20 optimal weight: 0.9990 chunk 44 optimal weight: 0.0060 chunk 13 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.180397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.119437 restraints weight = 20170.396| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 5.17 r_work: 0.3122 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4162 Z= 0.196 Angle : 0.533 9.025 5630 Z= 0.276 Chirality : 0.037 0.134 633 Planarity : 0.004 0.039 703 Dihedral : 4.626 38.947 563 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.06 % Allowed : 19.95 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 2.84 (0.38), residues: 504 helix: 3.48 (0.28), residues: 257 sheet: -0.10 (0.51), residues: 106 loop : 0.47 (0.56), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 97 HIS 0.002 0.001 HIS H 38 PHE 0.051 0.002 PHE L 84 TYR 0.011 0.001 TYR L 92 ARG 0.002 0.000 ARG A 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3836.12 seconds wall clock time: 66 minutes 6.03 seconds (3966.03 seconds total)