Starting phenix.real_space_refine on Wed Mar 5 16:17:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bhb_44539/03_2025/9bhb_44539.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bhb_44539/03_2025/9bhb_44539.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bhb_44539/03_2025/9bhb_44539.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bhb_44539/03_2025/9bhb_44539.map" model { file = "/net/cci-nas-00/data/ceres_data/9bhb_44539/03_2025/9bhb_44539.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bhb_44539/03_2025/9bhb_44539.cif" } resolution = 3.1 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= 0.009 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: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 1681 2.51 5 N 441 2.21 5 O 494 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 2626 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 931 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "K" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 841 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 103} Chain: "A" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 854 Classifications: {'peptide': 98} Link IDs: {'TRANS': 97} Chain breaks: 3 Time building chain proxies: 2.52, per 1000 atoms: 0.96 Number of scatterers: 2626 At special positions: 0 Unit cell: (55.1, 64.525, 91.35, 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 10 16.00 O 494 8.00 N 441 7.00 C 1681 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " 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: 0.55 Conformation dependent library (CDL) restraints added in 277.1 milliseconds 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 612 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 7 sheets defined 29.9% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.516A pdb=" N PHE H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.781A pdb=" N ASP H 86 " --> pdb=" O ARG H 83 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR H 87 " --> pdb=" O ASP H 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 83 through 87' Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.964A pdb=" N PHE K 83 " --> pdb=" O SER K 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 600 Processing helix chain 'A' and resid 622 through 640 removed outlier: 3.771A pdb=" N LYS A 638 " --> pdb=" O ASN A 634 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL A 639 " --> pdb=" O GLU A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 672 removed outlier: 4.278A pdb=" N GLU A 671 " --> pdb=" O HIS A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 693 removed outlier: 3.777A pdb=" N TRP A 678 " --> pdb=" O LYS A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 717 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.560A pdb=" N ALA H 10 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER H 110 " --> pdb=" O ALA H 10 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.560A pdb=" N ALA H 10 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER H 110 " --> pdb=" O ALA H 10 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 17 through 20 removed outlier: 3.540A pdb=" N LEU H 80 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 4 through 5 Processing sheet with id=AA6, first strand: chain 'K' and resid 10 through 12 removed outlier: 5.869A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE K 48 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 19 through 20 113 hydrogen bonds defined for protein. 297 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: 0.65 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 812 1.34 - 1.46: 562 1.46 - 1.57: 1300 1.57 - 1.69: 0 1.69 - 1.81: 14 Bond restraints: 2688 Sorted by residual: bond pdb=" N SER K 7 " pdb=" CA SER K 7 " ideal model delta sigma weight residual 1.461 1.489 -0.028 9.20e-03 1.18e+04 9.51e+00 bond pdb=" N VAL K 3 " pdb=" CA VAL K 3 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.27e-02 6.20e+03 8.23e+00 bond pdb=" N GLU K 17 " pdb=" CA GLU K 17 " ideal model delta sigma weight residual 1.454 1.487 -0.032 1.16e-02 7.43e+03 7.79e+00 bond pdb=" N LEU K 13 " pdb=" CA LEU K 13 " ideal model delta sigma weight residual 1.454 1.488 -0.033 1.27e-02 6.20e+03 6.85e+00 bond pdb=" N ASP K 18 " pdb=" CA ASP K 18 " ideal model delta sigma weight residual 1.455 1.490 -0.034 1.33e-02 5.65e+03 6.59e+00 ... (remaining 2683 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 3365 1.42 - 2.84: 217 2.84 - 4.25: 35 4.25 - 5.67: 9 5.67 - 7.09: 4 Bond angle restraints: 3630 Sorted by residual: angle pdb=" N ILE H 53 " pdb=" CA ILE H 53 " pdb=" C ILE H 53 " ideal model delta sigma weight residual 109.34 102.25 7.09 2.08e+00 2.31e-01 1.16e+01 angle pdb=" C ASP K 50 " pdb=" N ALA K 51 " pdb=" CA ALA K 51 " ideal model delta sigma weight residual 121.54 127.71 -6.17 1.91e+00 2.74e-01 1.04e+01 angle pdb=" CA THR K 5 " pdb=" CB THR K 5 " pdb=" OG1 THR K 5 " ideal model delta sigma weight residual 109.60 105.02 4.58 1.50e+00 4.44e-01 9.33e+00 angle pdb=" CG MET A 669 " pdb=" SD MET A 669 " pdb=" CE MET A 669 " ideal model delta sigma weight residual 100.90 94.18 6.72 2.20e+00 2.07e-01 9.32e+00 angle pdb=" CA GLN K 6 " pdb=" C GLN K 6 " pdb=" O GLN K 6 " ideal model delta sigma weight residual 121.58 118.25 3.33 1.12e+00 7.97e-01 8.84e+00 ... (remaining 3625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.67: 1407 15.67 - 31.33: 128 31.33 - 46.99: 38 46.99 - 62.66: 6 62.66 - 78.32: 3 Dihedral angle restraints: 1582 sinusoidal: 634 harmonic: 948 Sorted by residual: dihedral pdb=" CA MET A 669 " pdb=" C MET A 669 " pdb=" N LYS A 670 " pdb=" CA LYS A 670 " ideal model delta harmonic sigma weight residual 180.00 156.54 23.46 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA LEU A 657 " pdb=" C LEU A 657 " pdb=" N ASN A 658 " pdb=" CA ASN A 658 " ideal model delta harmonic sigma weight residual 180.00 -160.90 -19.10 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CB MET H 34 " pdb=" CG MET H 34 " pdb=" SD MET H 34 " pdb=" CE MET H 34 " ideal model delta sinusoidal sigma weight residual 60.00 119.06 -59.06 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 256 0.044 - 0.089: 94 0.089 - 0.133: 27 0.133 - 0.177: 8 0.177 - 0.222: 3 Chirality restraints: 388 Sorted by residual: chirality pdb=" CA ILE H 53 " pdb=" N ILE H 53 " pdb=" C ILE H 53 " pdb=" CB ILE H 53 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ILE K 48 " pdb=" N ILE K 48 " pdb=" C ILE K 48 " pdb=" CB ILE K 48 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.29e-01 chirality pdb=" CA ILE K 2 " pdb=" N ILE K 2 " pdb=" C ILE K 2 " pdb=" CB ILE K 2 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.59e-01 ... (remaining 385 not shown) Planarity restraints: 456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 67 " -0.001 2.00e-02 2.50e+03 1.97e-02 6.82e+00 pdb=" CG PHE H 67 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE H 67 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE H 67 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE H 67 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE H 67 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE H 67 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 96 " -0.010 2.00e-02 2.50e+03 1.08e-02 2.90e+00 pdb=" CG TRP K 96 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP K 96 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP K 96 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP K 96 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP K 96 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP K 96 " 0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 96 " -0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 96 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP K 96 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 96 " -0.027 5.00e-02 4.00e+02 4.16e-02 2.76e+00 pdb=" N PRO H 97 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO H 97 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 97 " -0.023 5.00e-02 4.00e+02 ... (remaining 453 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 671 2.80 - 3.32: 2173 3.32 - 3.85: 4469 3.85 - 4.37: 5120 4.37 - 4.90: 9233 Nonbonded interactions: 21666 Sorted by model distance: nonbonded pdb=" OE1 GLU H 33 " pdb=" OH TYR H 50 " model vdw 2.274 3.040 nonbonded pdb=" O TYR K 49 " pdb=" OH TYR K 91 " model vdw 2.304 3.040 nonbonded pdb=" O ASP K 82 " pdb=" OH TYR K 86 " model vdw 2.332 3.040 nonbonded pdb=" OH TYR H 99 " pdb=" OE2 GLU A 675 " model vdw 2.363 3.040 nonbonded pdb=" NH1 ARG K 54 " pdb=" O ILE K 58 " model vdw 2.380 3.120 ... (remaining 21661 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.870 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.660 Find NCS groups from input model: 0.030 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 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 0.058 2688 Z= 0.388 Angle : 0.815 7.089 3630 Z= 0.480 Chirality : 0.054 0.222 388 Planarity : 0.006 0.042 456 Dihedral : 13.801 78.321 964 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 0.35 % Allowed : 1.41 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.45), residues: 316 helix: -1.44 (0.45), residues: 77 sheet: -1.17 (0.59), residues: 92 loop : -1.39 (0.49), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP K 96 HIS 0.004 0.001 HIS A 667 PHE 0.034 0.003 PHE H 67 TYR 0.010 0.002 TYR K 49 ARG 0.005 0.001 ARG K 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.292 Fit side-chains REVERT: H 83 ARG cc_start: 0.7425 (mtt180) cc_final: 0.6945 (mtt-85) REVERT: K 100 GLN cc_start: 0.8370 (mp10) cc_final: 0.8087 (mp10) REVERT: A 680 LYS cc_start: 0.8178 (mtpt) cc_final: 0.7557 (mmmt) REVERT: A 706 LYS cc_start: 0.7845 (tppt) cc_final: 0.7386 (tmtt) outliers start: 1 outliers final: 0 residues processed: 44 average time/residue: 0.1767 time to fit residues: 9.2038 Evaluate side-chains 42 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 0.0470 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN K 6 GLN K 38 HIS A 600 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.155915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.134120 restraints weight = 2928.518| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.89 r_work: 0.3405 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2688 Z= 0.233 Angle : 0.510 4.625 3630 Z= 0.280 Chirality : 0.041 0.157 388 Planarity : 0.004 0.032 456 Dihedral : 4.208 19.301 351 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.06 % Allowed : 8.10 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.47), residues: 316 helix: 0.79 (0.50), residues: 77 sheet: -1.01 (0.54), residues: 104 loop : -0.73 (0.55), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 79 HIS 0.002 0.001 HIS A 660 PHE 0.009 0.002 PHE K 83 TYR 0.009 0.001 TYR K 49 ARG 0.004 0.001 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.292 Fit side-chains REVERT: H 83 ARG cc_start: 0.7656 (mtt180) cc_final: 0.7101 (mtt-85) REVERT: A 680 LYS cc_start: 0.8222 (mtpt) cc_final: 0.7580 (mmmt) REVERT: A 706 LYS cc_start: 0.7838 (tppt) cc_final: 0.7220 (tmtt) outliers start: 3 outliers final: 1 residues processed: 46 average time/residue: 0.2173 time to fit residues: 11.5052 Evaluate side-chains 45 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 102 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 21 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 0.1980 chunk 7 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 38 HIS A 600 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.157355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.136130 restraints weight = 2887.677| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.83 r_work: 0.3296 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2688 Z= 0.252 Angle : 0.499 4.630 3630 Z= 0.271 Chirality : 0.041 0.159 388 Planarity : 0.003 0.031 456 Dihedral : 4.142 17.435 351 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.41 % Allowed : 10.56 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.49), residues: 316 helix: 1.49 (0.53), residues: 82 sheet: -0.65 (0.55), residues: 101 loop : -0.63 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 79 HIS 0.003 0.001 HIS A 660 PHE 0.010 0.002 PHE K 83 TYR 0.010 0.001 TYR K 49 ARG 0.003 0.000 ARG K 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: H 83 ARG cc_start: 0.7605 (mtt180) cc_final: 0.7092 (mtt-85) REVERT: A 680 LYS cc_start: 0.8189 (mtpt) cc_final: 0.7630 (mmmt) REVERT: A 706 LYS cc_start: 0.7899 (tppt) cc_final: 0.7292 (tmtt) outliers start: 4 outliers final: 4 residues processed: 48 average time/residue: 0.2061 time to fit residues: 11.5133 Evaluate side-chains 50 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 52 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 5 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 0.2980 chunk 16 optimal weight: 0.0010 chunk 26 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 chunk 15 optimal weight: 0.0770 overall best weight: 0.2744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 38 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.160910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.139975 restraints weight = 2861.185| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.79 r_work: 0.3361 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2688 Z= 0.139 Angle : 0.419 4.665 3630 Z= 0.229 Chirality : 0.038 0.155 388 Planarity : 0.003 0.032 456 Dihedral : 3.764 15.435 351 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.11 % Allowed : 13.38 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.50), residues: 316 helix: 2.36 (0.54), residues: 83 sheet: -0.53 (0.55), residues: 102 loop : -0.59 (0.57), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 79 HIS 0.002 0.001 HIS A 660 PHE 0.007 0.001 PHE H 67 TYR 0.009 0.001 TYR K 91 ARG 0.002 0.000 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: H 83 ARG cc_start: 0.7542 (mtt180) cc_final: 0.7030 (mtt-85) REVERT: K 6 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7705 (mt0) REVERT: A 680 LYS cc_start: 0.8141 (mtpt) cc_final: 0.7608 (mmmt) REVERT: A 706 LYS cc_start: 0.7860 (tppt) cc_final: 0.7256 (tmtt) outliers start: 6 outliers final: 3 residues processed: 49 average time/residue: 0.1917 time to fit residues: 11.0606 Evaluate side-chains 49 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 75 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 0.0970 chunk 18 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 38 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.151377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.129563 restraints weight = 2927.455| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.94 r_work: 0.3298 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2688 Z= 0.241 Angle : 0.467 4.642 3630 Z= 0.252 Chirality : 0.040 0.159 388 Planarity : 0.003 0.029 456 Dihedral : 3.941 15.763 351 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.46 % Allowed : 12.68 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.50), residues: 316 helix: 2.51 (0.54), residues: 82 sheet: -0.53 (0.55), residues: 102 loop : -0.58 (0.57), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 96 HIS 0.003 0.001 HIS A 660 PHE 0.010 0.002 PHE K 83 TYR 0.010 0.001 TYR K 49 ARG 0.003 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: H 19 ARG cc_start: 0.8065 (ttp-110) cc_final: 0.7837 (mtp85) REVERT: H 31 ASP cc_start: 0.8260 (t0) cc_final: 0.7479 (t0) REVERT: H 83 ARG cc_start: 0.7668 (mtt180) cc_final: 0.7096 (mtt-85) REVERT: A 680 LYS cc_start: 0.8277 (mtpt) cc_final: 0.7737 (mmmt) REVERT: A 706 LYS cc_start: 0.7856 (tppt) cc_final: 0.7228 (tmtt) outliers start: 7 outliers final: 4 residues processed: 48 average time/residue: 0.1872 time to fit residues: 10.4801 Evaluate side-chains 47 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain K residue 5 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 19 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.147422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.125130 restraints weight = 3026.096| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.99 r_work: 0.3284 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 2688 Z= 0.301 Angle : 0.514 4.660 3630 Z= 0.275 Chirality : 0.042 0.166 388 Planarity : 0.003 0.027 456 Dihedral : 4.213 15.778 351 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.23 % Allowed : 12.32 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.50), residues: 316 helix: 2.45 (0.54), residues: 82 sheet: -0.55 (0.55), residues: 99 loop : -0.48 (0.57), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 96 HIS 0.004 0.001 HIS A 660 PHE 0.011 0.002 PHE K 83 TYR 0.010 0.001 TYR K 49 ARG 0.002 0.000 ARG K 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: H 31 ASP cc_start: 0.8296 (t0) cc_final: 0.7527 (t0) REVERT: H 83 ARG cc_start: 0.7644 (mtt180) cc_final: 0.7140 (mtt-85) REVERT: K 6 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.7834 (mt0) REVERT: A 680 LYS cc_start: 0.8073 (mtpt) cc_final: 0.7564 (mmmt) REVERT: A 706 LYS cc_start: 0.7851 (tppt) cc_final: 0.7202 (tmtt) outliers start: 12 outliers final: 9 residues processed: 55 average time/residue: 0.1799 time to fit residues: 11.6259 Evaluate side-chains 54 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 6 optimal weight: 0.0980 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 38 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.155559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.132944 restraints weight = 2987.751| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.00 r_work: 0.3325 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2688 Z= 0.220 Angle : 0.473 4.656 3630 Z= 0.254 Chirality : 0.040 0.163 388 Planarity : 0.003 0.027 456 Dihedral : 4.005 15.583 351 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.17 % Allowed : 14.44 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.50), residues: 316 helix: 2.71 (0.54), residues: 82 sheet: -0.52 (0.54), residues: 99 loop : -0.44 (0.57), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 79 HIS 0.002 0.001 HIS A 660 PHE 0.011 0.002 PHE K 83 TYR 0.008 0.001 TYR K 49 ARG 0.002 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: H 31 ASP cc_start: 0.8314 (t0) cc_final: 0.7586 (t0) REVERT: H 83 ARG cc_start: 0.7657 (mtt180) cc_final: 0.7125 (mtt-85) REVERT: K 6 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.7835 (mt0) REVERT: K 93 ASN cc_start: 0.7472 (p0) cc_final: 0.6555 (t0) REVERT: A 680 LYS cc_start: 0.8245 (mtpt) cc_final: 0.7710 (mmmt) REVERT: A 706 LYS cc_start: 0.7915 (tppt) cc_final: 0.7285 (tmtt) outliers start: 9 outliers final: 7 residues processed: 50 average time/residue: 0.1880 time to fit residues: 11.0656 Evaluate side-chains 51 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain A residue 672 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 21 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 38 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.152450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.130190 restraints weight = 2936.580| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.91 r_work: 0.3305 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2688 Z= 0.285 Angle : 0.509 4.679 3630 Z= 0.273 Chirality : 0.041 0.165 388 Planarity : 0.003 0.026 456 Dihedral : 4.154 16.083 351 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 4.93 % Allowed : 12.32 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.50), residues: 316 helix: 2.63 (0.54), residues: 82 sheet: -0.57 (0.54), residues: 98 loop : -0.38 (0.57), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 79 HIS 0.003 0.001 HIS A 660 PHE 0.013 0.002 PHE K 83 TYR 0.010 0.001 TYR K 49 ARG 0.002 0.000 ARG K 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: H 31 ASP cc_start: 0.8382 (t0) cc_final: 0.7659 (t0) REVERT: H 33 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6784 (mt-10) REVERT: H 83 ARG cc_start: 0.7759 (mtt180) cc_final: 0.7269 (mtt-85) REVERT: K 6 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.7962 (mt0) REVERT: A 657 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8030 (mt) REVERT: A 680 LYS cc_start: 0.8335 (mtpt) cc_final: 0.7854 (mmmt) REVERT: A 706 LYS cc_start: 0.7999 (tppt) cc_final: 0.7384 (tmtt) outliers start: 14 outliers final: 9 residues processed: 55 average time/residue: 0.1785 time to fit residues: 11.4712 Evaluate side-chains 54 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 672 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 22 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 0.0670 chunk 23 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 38 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.152356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.129481 restraints weight = 2962.244| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.04 r_work: 0.3340 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2688 Z= 0.201 Angle : 0.470 4.668 3630 Z= 0.253 Chirality : 0.039 0.163 388 Planarity : 0.003 0.027 456 Dihedral : 3.962 15.764 351 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.23 % Allowed : 13.73 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.50), residues: 316 helix: 2.90 (0.54), residues: 82 sheet: -0.44 (0.54), residues: 98 loop : -0.34 (0.57), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 79 HIS 0.002 0.001 HIS A 660 PHE 0.011 0.001 PHE K 83 TYR 0.007 0.001 TYR K 91 ARG 0.005 0.000 ARG K 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: H 31 ASP cc_start: 0.8245 (t0) cc_final: 0.7503 (t0) REVERT: H 33 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6646 (mt-10) REVERT: H 83 ARG cc_start: 0.7595 (mtt180) cc_final: 0.7115 (mtt-85) REVERT: K 6 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7717 (mt0) REVERT: K 93 ASN cc_start: 0.7409 (p0) cc_final: 0.6574 (t0) REVERT: A 657 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7958 (mt) REVERT: A 680 LYS cc_start: 0.8127 (mtpt) cc_final: 0.7615 (mmmt) REVERT: A 706 LYS cc_start: 0.7885 (tppt) cc_final: 0.7248 (tmtt) outliers start: 12 outliers final: 7 residues processed: 51 average time/residue: 0.1672 time to fit residues: 10.0462 Evaluate side-chains 52 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 672 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 23 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 28 optimal weight: 0.3980 chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 0.2980 chunk 16 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 38 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.150900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.127668 restraints weight = 2983.856| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.08 r_work: 0.3328 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2688 Z= 0.236 Angle : 0.489 4.752 3630 Z= 0.262 Chirality : 0.040 0.161 388 Planarity : 0.003 0.027 456 Dihedral : 4.011 17.496 351 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.87 % Allowed : 13.73 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.50), residues: 316 helix: 2.93 (0.54), residues: 82 sheet: -0.41 (0.54), residues: 98 loop : -0.31 (0.58), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 79 HIS 0.003 0.001 HIS A 660 PHE 0.010 0.002 PHE K 83 TYR 0.009 0.001 TYR K 49 ARG 0.006 0.000 ARG K 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: H 31 ASP cc_start: 0.8254 (t0) cc_final: 0.7515 (t0) REVERT: H 33 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6642 (mt-10) REVERT: H 83 ARG cc_start: 0.7613 (mtt180) cc_final: 0.7125 (mtt-85) REVERT: K 6 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7740 (mt0) REVERT: K 93 ASN cc_start: 0.7420 (p0) cc_final: 0.6582 (t0) REVERT: A 657 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7983 (mt) REVERT: A 674 LYS cc_start: 0.7832 (mttt) cc_final: 0.7117 (tttt) REVERT: A 680 LYS cc_start: 0.8126 (mtpt) cc_final: 0.7613 (mmmt) REVERT: A 706 LYS cc_start: 0.7888 (tppt) cc_final: 0.7241 (tmtt) outliers start: 11 outliers final: 7 residues processed: 51 average time/residue: 0.2098 time to fit residues: 12.5118 Evaluate side-chains 50 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 672 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 12 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3697 r_free = 0.3697 target = 0.152128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.130169 restraints weight = 2949.508| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.92 r_work: 0.3282 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2688 Z= 0.278 Angle : 0.510 4.783 3630 Z= 0.274 Chirality : 0.041 0.165 388 Planarity : 0.003 0.026 456 Dihedral : 4.161 18.237 351 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.87 % Allowed : 14.08 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.50), residues: 316 helix: 2.81 (0.54), residues: 82 sheet: -0.45 (0.54), residues: 98 loop : -0.30 (0.58), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 79 HIS 0.003 0.001 HIS A 660 PHE 0.014 0.002 PHE K 83 TYR 0.009 0.001 TYR K 49 ARG 0.005 0.000 ARG K 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1786.79 seconds wall clock time: 31 minutes 46.52 seconds (1906.52 seconds total)