Starting phenix.real_space_refine on Sat Apr 26 17:22:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9knw_62464/04_2025/9knw_62464.cif Found real_map, /net/cci-nas-00/data/ceres_data/9knw_62464/04_2025/9knw_62464.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9knw_62464/04_2025/9knw_62464.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9knw_62464/04_2025/9knw_62464.map" model { file = "/net/cci-nas-00/data/ceres_data/9knw_62464/04_2025/9knw_62464.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9knw_62464/04_2025/9knw_62464.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 17 5.16 5 C 1783 2.51 5 N 460 2.21 5 O 484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 2747 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1000 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 118} Chain: "A" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 745 Classifications: {'peptide': 93} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 88} Chain: "C" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 879 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 89 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'PC8': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.93, per 1000 atoms: 1.07 Number of scatterers: 2747 At special positions: 0 Unit cell: (81.51, 93.48, 86.07, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 17 16.00 P 3 15.00 O 484 8.00 N 460 7.00 C 1783 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 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: 0.81 Conformation dependent library (CDL) restraints added in 319.9 milliseconds 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 614 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 2 sheets defined 60.4% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 28 through 33 Processing helix chain 'B' and resid 40 through 57 removed outlier: 3.789A pdb=" N TRP B 44 " --> pdb=" O THR B 40 " (cutoff:3.500A) Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 63 through 67 Processing helix chain 'B' and resid 68 through 86 Processing helix chain 'B' and resid 93 through 126 removed outlier: 3.688A pdb=" N HIS B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 23 removed outlier: 3.988A pdb=" N MET A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 29 removed outlier: 4.055A pdb=" N TRP A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 34 through 44 removed outlier: 3.521A pdb=" N ILE A 38 " --> pdb=" O TRP A 34 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 46 No H-bonds generated for 'chain 'A' and resid 45 through 46' Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.647A pdb=" N ILE A 50 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 73 Processing helix chain 'A' and resid 77 through 108 removed outlier: 3.695A pdb=" N PHE A 81 " --> pdb=" O ASN A 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.514A pdb=" N THR C 91 " --> pdb=" O PRO C 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.104A pdb=" N GLY C 10 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N SER C 114 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL C 12 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) 166 hydrogen bonds defined for protein. 465 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: 0.67 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 409 1.30 - 1.43: 778 1.43 - 1.55: 1578 1.55 - 1.68: 20 1.68 - 1.81: 29 Bond restraints: 2814 Sorted by residual: bond pdb=" CB7 CDL B 201 " pdb=" OB8 CDL B 201 " ideal model delta sigma weight residual 1.334 1.436 -0.102 1.10e-02 8.26e+03 8.58e+01 bond pdb=" CA7 CDL B 201 " pdb=" OA8 CDL B 201 " ideal model delta sigma weight residual 1.334 1.430 -0.096 1.10e-02 8.26e+03 7.60e+01 bond pdb=" CA5 CDL B 201 " pdb=" OA6 CDL B 201 " ideal model delta sigma weight residual 1.342 1.440 -0.098 1.50e-02 4.44e+03 4.28e+01 bond pdb=" CB5 CDL B 201 " pdb=" OB6 CDL B 201 " ideal model delta sigma weight residual 1.342 1.438 -0.096 1.50e-02 4.44e+03 4.11e+01 bond pdb=" OB2 CDL B 201 " pdb=" PB2 CDL B 201 " ideal model delta sigma weight residual 1.579 1.664 -0.085 1.50e-02 4.44e+03 3.22e+01 ... (remaining 2809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 3736 3.13 - 6.25: 40 6.25 - 9.38: 8 9.38 - 12.51: 2 12.51 - 15.63: 1 Bond angle restraints: 3787 Sorted by residual: angle pdb=" C51 CDL B 201 " pdb=" CB5 CDL B 201 " pdb=" OB6 CDL B 201 " ideal model delta sigma weight residual 111.33 120.44 -9.11 1.32e+00 5.72e-01 4.75e+01 angle pdb=" C11 CDL B 201 " pdb=" CA5 CDL B 201 " pdb=" OA6 CDL B 201 " ideal model delta sigma weight residual 111.33 119.87 -8.54 1.32e+00 5.72e-01 4.17e+01 angle pdb=" C71 CDL B 201 " pdb=" CB7 CDL B 201 " pdb=" OB8 CDL B 201 " ideal model delta sigma weight residual 111.64 121.12 -9.48 1.65e+00 3.69e-01 3.32e+01 angle pdb=" CA2 CDL B 201 " pdb=" OA2 CDL B 201 " pdb=" PA1 CDL B 201 " ideal model delta sigma weight residual 121.27 115.75 5.52 1.00e+00 1.00e+00 3.05e+01 angle pdb=" C31 CDL B 201 " pdb=" CA7 CDL B 201 " pdb=" OA8 CDL B 201 " ideal model delta sigma weight residual 111.64 120.45 -8.81 1.65e+00 3.69e-01 2.86e+01 ... (remaining 3782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.66: 1562 29.66 - 59.32: 125 59.32 - 88.98: 5 88.98 - 118.64: 0 118.64 - 148.30: 1 Dihedral angle restraints: 1693 sinusoidal: 734 harmonic: 959 Sorted by residual: dihedral pdb=" C1 PC8 A 201 " pdb=" O3 PC8 A 201 " pdb=" P1 PC8 A 201 " pdb=" O4 PC8 A 201 " ideal model delta sinusoidal sigma weight residual 166.83 -44.87 -148.30 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 96 " pdb=" CB CYS C 96 " ideal model delta sinusoidal sigma weight residual -86.00 -118.46 32.46 1 1.00e+01 1.00e-02 1.50e+01 dihedral pdb=" CA GLU A 49 " pdb=" CB GLU A 49 " pdb=" CG GLU A 49 " pdb=" CD GLU A 49 " ideal model delta sinusoidal sigma weight residual 60.00 118.30 -58.30 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 1690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 282 0.042 - 0.083: 83 0.083 - 0.124: 20 0.124 - 0.165: 6 0.165 - 0.207: 1 Chirality restraints: 392 Sorted by residual: chirality pdb=" C7 PC8 A 201 " pdb=" C6 PC8 A 201 " pdb=" C8 PC8 A 201 " pdb=" O7 PC8 A 201 " both_signs ideal model delta sigma weight residual False -2.32 -2.53 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA PHE A 66 " pdb=" N PHE A 66 " pdb=" C PHE A 66 " pdb=" CB PHE A 66 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA GLU B 21 " pdb=" N GLU B 21 " pdb=" C GLU B 21 " pdb=" CB GLU B 21 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.73e-01 ... (remaining 389 not shown) Planarity restraints: 464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 34 " -0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO B 35 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 35 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 35 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 66 " -0.015 2.00e-02 2.50e+03 1.31e-02 3.00e+00 pdb=" CG PHE A 66 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE A 66 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 66 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 66 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE A 66 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 66 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 29 " 0.026 5.00e-02 4.00e+02 3.86e-02 2.39e+00 pdb=" N PRO A 30 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 30 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 30 " 0.022 5.00e-02 4.00e+02 ... (remaining 461 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 852 2.82 - 3.34: 2563 3.34 - 3.86: 4571 3.86 - 4.38: 5225 4.38 - 4.90: 8698 Nonbonded interactions: 21909 Sorted by model distance: nonbonded pdb=" NH1 ARG C 38 " pdb=" OD1 ASP C 90 " model vdw 2.299 3.120 nonbonded pdb=" NE2 GLN C 13 " pdb=" O SER C 114 " model vdw 2.326 3.120 nonbonded pdb=" NE1 TRP B 82 " pdb=" O GLY A 29 " model vdw 2.337 3.120 nonbonded pdb=" OD1 ASP C 52 " pdb=" N SER C 57 " model vdw 2.339 3.120 nonbonded pdb=" N ASP A 17 " pdb=" OD1 ASP A 17 " model vdw 2.354 3.120 ... (remaining 21904 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: 2.140 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.490 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.106 2815 Z= 0.524 Angle : 0.932 15.635 3789 Z= 0.523 Chirality : 0.044 0.207 392 Planarity : 0.005 0.045 464 Dihedral : 19.172 148.303 1076 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.48 % Allowed : 17.41 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -1.35 (0.42), residues: 327 helix: -0.39 (0.35), residues: 169 sheet: -1.23 (0.64), residues: 57 loop : -1.25 (0.60), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 28 HIS 0.005 0.001 HIS A 84 PHE 0.027 0.002 PHE A 66 TYR 0.018 0.002 TYR C 95 ARG 0.002 0.000 ARG B 29 Details of bonding type rmsd hydrogen bonds : bond 0.11730 ( 166) hydrogen bonds : angle 5.43762 ( 465) SS BOND : bond 0.00508 ( 1) SS BOND : angle 1.10010 ( 2) covalent geometry : bond 0.00908 ( 2814) covalent geometry : angle 0.93148 ( 3787) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7769 (tt0) REVERT: A 18 PHE cc_start: 0.6364 (t80) cc_final: 0.6059 (p90) outliers start: 4 outliers final: 4 residues processed: 87 average time/residue: 0.2261 time to fit residues: 22.2236 Evaluate side-chains 76 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 25 optimal weight: 0.0050 chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.193529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.157763 restraints weight = 3830.235| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.92 r_work: 0.3737 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2815 Z= 0.128 Angle : 0.550 7.602 3789 Z= 0.282 Chirality : 0.040 0.131 392 Planarity : 0.005 0.053 464 Dihedral : 16.408 113.890 483 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.59 % Allowed : 24.07 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.70 (0.46), residues: 327 helix: 1.44 (0.38), residues: 178 sheet: -0.72 (0.74), residues: 49 loop : -0.55 (0.63), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 36 HIS 0.004 0.001 HIS A 84 PHE 0.012 0.001 PHE A 69 TYR 0.010 0.001 TYR C 95 ARG 0.009 0.001 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03632 ( 166) hydrogen bonds : angle 4.42144 ( 465) SS BOND : bond 0.00476 ( 1) SS BOND : angle 0.93089 ( 2) covalent geometry : bond 0.00288 ( 2814) covalent geometry : angle 0.54975 ( 3787) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7631 (tt0) REVERT: C 43 LYS cc_start: 0.6547 (ttpt) cc_final: 0.6302 (ttpt) REVERT: C 102 TRP cc_start: 0.6142 (t-100) cc_final: 0.5805 (m-90) outliers start: 7 outliers final: 6 residues processed: 78 average time/residue: 0.2119 time to fit residues: 18.7467 Evaluate side-chains 77 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain C residue 12 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 15 optimal weight: 0.0670 chunk 28 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN C 54 GLN C 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.193671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.158537 restraints weight = 3797.004| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.85 r_work: 0.3760 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2815 Z= 0.120 Angle : 0.510 5.917 3789 Z= 0.264 Chirality : 0.040 0.141 392 Planarity : 0.005 0.063 464 Dihedral : 14.190 75.466 476 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.44 % Allowed : 24.07 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.31 (0.48), residues: 327 helix: 2.00 (0.39), residues: 180 sheet: -1.34 (0.70), residues: 50 loop : 0.10 (0.66), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 36 HIS 0.003 0.001 HIS A 84 PHE 0.012 0.001 PHE A 69 TYR 0.011 0.001 TYR C 95 ARG 0.003 0.001 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03315 ( 166) hydrogen bonds : angle 4.31743 ( 465) SS BOND : bond 0.00929 ( 1) SS BOND : angle 0.69176 ( 2) covalent geometry : bond 0.00270 ( 2814) covalent geometry : angle 0.51033 ( 3787) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.292 Fit side-chains REVERT: B 26 GLU cc_start: 0.6851 (mp0) cc_final: 0.6539 (mp0) REVERT: B 119 GLN cc_start: 0.8045 (mm-40) cc_final: 0.7600 (tt0) REVERT: A 19 ARG cc_start: 0.7812 (ptt-90) cc_final: 0.6911 (ptt-90) outliers start: 12 outliers final: 10 residues processed: 79 average time/residue: 0.1993 time to fit residues: 18.0407 Evaluate side-chains 79 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 31 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 22 optimal weight: 0.0050 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 6 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 GLN ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.195398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.160579 restraints weight = 3819.844| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.90 r_work: 0.3787 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2815 Z= 0.109 Angle : 0.504 8.278 3789 Z= 0.259 Chirality : 0.040 0.136 392 Planarity : 0.005 0.060 464 Dihedral : 13.290 67.444 476 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 4.81 % Allowed : 24.44 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.68 (0.49), residues: 327 helix: 2.24 (0.39), residues: 180 sheet: -1.38 (0.72), residues: 50 loop : 0.52 (0.70), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 36 HIS 0.003 0.001 HIS A 84 PHE 0.011 0.001 PHE A 69 TYR 0.012 0.001 TYR C 95 ARG 0.002 0.000 ARG B 29 Details of bonding type rmsd hydrogen bonds : bond 0.03177 ( 166) hydrogen bonds : angle 4.18800 ( 465) SS BOND : bond 0.01114 ( 1) SS BOND : angle 0.62545 ( 2) covalent geometry : bond 0.00242 ( 2814) covalent geometry : angle 0.50363 ( 3787) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.270 Fit side-chains REVERT: B 119 GLN cc_start: 0.8050 (mm-40) cc_final: 0.7612 (tt0) REVERT: A 19 ARG cc_start: 0.7793 (ptt-90) cc_final: 0.6969 (ptt-90) REVERT: C 4 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7328 (tp) REVERT: C 43 LYS cc_start: 0.6373 (ttpt) cc_final: 0.6157 (ttpt) outliers start: 13 outliers final: 10 residues processed: 76 average time/residue: 0.2134 time to fit residues: 18.4523 Evaluate side-chains 77 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 GLN C 54 GLN C 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.194038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.159614 restraints weight = 3846.217| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.82 r_work: 0.3778 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2815 Z= 0.125 Angle : 0.518 8.199 3789 Z= 0.265 Chirality : 0.040 0.126 392 Planarity : 0.007 0.093 464 Dihedral : 13.044 65.089 476 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 5.56 % Allowed : 24.07 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.95 (0.50), residues: 327 helix: 2.26 (0.39), residues: 180 sheet: -0.86 (0.71), residues: 56 loop : 0.97 (0.75), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 36 HIS 0.005 0.001 HIS A 84 PHE 0.013 0.001 PHE A 69 TYR 0.012 0.001 TYR C 95 ARG 0.008 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03293 ( 166) hydrogen bonds : angle 4.18554 ( 465) SS BOND : bond 0.00504 ( 1) SS BOND : angle 0.40228 ( 2) covalent geometry : bond 0.00290 ( 2814) covalent geometry : angle 0.51812 ( 3787) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.359 Fit side-chains REVERT: B 119 GLN cc_start: 0.8066 (mm-40) cc_final: 0.7623 (tt0) REVERT: A 19 ARG cc_start: 0.7845 (ptt-90) cc_final: 0.6980 (ptt-90) REVERT: C 4 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7469 (tp) REVERT: C 43 LYS cc_start: 0.6400 (ttpt) cc_final: 0.6194 (ttpt) outliers start: 15 outliers final: 12 residues processed: 71 average time/residue: 0.1998 time to fit residues: 16.2825 Evaluate side-chains 75 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 9 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 14 optimal weight: 0.1980 chunk 30 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.194568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.160269 restraints weight = 3815.666| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 2.79 r_work: 0.3785 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2815 Z= 0.116 Angle : 0.514 9.134 3789 Z= 0.263 Chirality : 0.040 0.125 392 Planarity : 0.005 0.064 464 Dihedral : 12.651 63.536 476 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 5.19 % Allowed : 24.44 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 2.04 (0.50), residues: 327 helix: 2.30 (0.39), residues: 180 sheet: -0.78 (0.76), residues: 49 loop : 0.89 (0.72), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 36 HIS 0.004 0.001 HIS A 84 PHE 0.011 0.001 PHE A 69 TYR 0.012 0.001 TYR C 95 ARG 0.007 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03319 ( 166) hydrogen bonds : angle 4.15315 ( 465) SS BOND : bond 0.00462 ( 1) SS BOND : angle 0.53680 ( 2) covalent geometry : bond 0.00265 ( 2814) covalent geometry : angle 0.51422 ( 3787) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.272 Fit side-chains REVERT: B 119 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7616 (tt0) REVERT: A 19 ARG cc_start: 0.7835 (ptt-90) cc_final: 0.7006 (ptt-90) outliers start: 14 outliers final: 10 residues processed: 73 average time/residue: 0.1956 time to fit residues: 16.2938 Evaluate side-chains 75 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 23 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 0.0970 chunk 20 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 ASN ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 GLN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.195288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.160883 restraints weight = 3927.363| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.85 r_work: 0.3784 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2815 Z= 0.116 Angle : 0.527 7.857 3789 Z= 0.268 Chirality : 0.040 0.124 392 Planarity : 0.005 0.057 464 Dihedral : 12.249 61.754 476 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 4.81 % Allowed : 23.70 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.81 (0.49), residues: 327 helix: 2.19 (0.38), residues: 180 sheet: -1.22 (0.67), residues: 56 loop : 1.03 (0.76), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 36 HIS 0.005 0.001 HIS A 84 PHE 0.010 0.001 PHE A 69 TYR 0.012 0.001 TYR C 95 ARG 0.009 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03325 ( 166) hydrogen bonds : angle 4.16890 ( 465) SS BOND : bond 0.00425 ( 1) SS BOND : angle 0.65102 ( 2) covalent geometry : bond 0.00266 ( 2814) covalent geometry : angle 0.52688 ( 3787) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.268 Fit side-chains REVERT: B 15 ARG cc_start: 0.7283 (ttp80) cc_final: 0.6994 (ptt90) REVERT: B 119 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7604 (tt0) REVERT: A 19 ARG cc_start: 0.7850 (ptt-90) cc_final: 0.7065 (ptt-90) outliers start: 13 outliers final: 11 residues processed: 71 average time/residue: 0.2016 time to fit residues: 16.3099 Evaluate side-chains 75 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.0570 chunk 9 optimal weight: 0.0010 chunk 22 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.9708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.194465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.159746 restraints weight = 3788.997| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.85 r_work: 0.3794 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2815 Z= 0.136 Angle : 0.572 8.935 3789 Z= 0.284 Chirality : 0.041 0.188 392 Planarity : 0.005 0.057 464 Dihedral : 12.228 61.116 476 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 4.44 % Allowed : 24.81 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.74 (0.49), residues: 327 helix: 2.18 (0.38), residues: 180 sheet: -1.38 (0.66), residues: 56 loop : 0.99 (0.75), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 36 HIS 0.005 0.001 HIS A 84 PHE 0.014 0.001 PHE A 69 TYR 0.012 0.001 TYR C 95 ARG 0.007 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03373 ( 166) hydrogen bonds : angle 4.16994 ( 465) SS BOND : bond 0.00494 ( 1) SS BOND : angle 0.67262 ( 2) covalent geometry : bond 0.00317 ( 2814) covalent geometry : angle 0.57229 ( 3787) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: B 119 GLN cc_start: 0.8040 (mm-40) cc_final: 0.7619 (tt0) outliers start: 12 outliers final: 10 residues processed: 71 average time/residue: 0.2016 time to fit residues: 16.3308 Evaluate side-chains 72 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 8 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 14 optimal weight: 0.0050 chunk 13 optimal weight: 0.8980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.195257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.161162 restraints weight = 3795.117| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.84 r_work: 0.3777 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2815 Z= 0.122 Angle : 0.571 8.756 3789 Z= 0.288 Chirality : 0.042 0.200 392 Planarity : 0.005 0.058 464 Dihedral : 11.961 60.010 476 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.70 % Allowed : 25.19 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.69 (0.49), residues: 327 helix: 2.27 (0.38), residues: 176 sheet: -1.59 (0.66), residues: 56 loop : 0.87 (0.74), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 36 HIS 0.005 0.001 HIS A 84 PHE 0.012 0.001 PHE A 69 TYR 0.012 0.001 TYR C 95 ARG 0.005 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03375 ( 166) hydrogen bonds : angle 4.17332 ( 465) SS BOND : bond 0.00604 ( 1) SS BOND : angle 0.60017 ( 2) covalent geometry : bond 0.00283 ( 2814) covalent geometry : angle 0.57134 ( 3787) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: B 15 ARG cc_start: 0.7266 (ttp80) cc_final: 0.6966 (ptt90) REVERT: B 119 GLN cc_start: 0.8030 (mm-40) cc_final: 0.7614 (tt0) REVERT: C 73 ASP cc_start: 0.6682 (t0) cc_final: 0.5746 (p0) outliers start: 10 outliers final: 10 residues processed: 70 average time/residue: 0.2073 time to fit residues: 16.6021 Evaluate side-chains 74 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 ASN ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.197422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.163749 restraints weight = 3871.013| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 2.79 r_work: 0.3872 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2815 Z= 0.119 Angle : 0.577 11.144 3789 Z= 0.287 Chirality : 0.042 0.187 392 Planarity : 0.005 0.058 464 Dihedral : 11.842 59.319 476 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.70 % Allowed : 25.56 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.71 (0.49), residues: 327 helix: 2.30 (0.38), residues: 176 sheet: -1.62 (0.67), residues: 56 loop : 0.89 (0.74), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 28 HIS 0.005 0.001 HIS A 84 PHE 0.011 0.001 PHE A 69 TYR 0.012 0.001 TYR C 95 ARG 0.007 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03340 ( 166) hydrogen bonds : angle 4.14529 ( 465) SS BOND : bond 0.00503 ( 1) SS BOND : angle 0.28538 ( 2) covalent geometry : bond 0.00275 ( 2814) covalent geometry : angle 0.57726 ( 3787) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: B 119 GLN cc_start: 0.8059 (mm-40) cc_final: 0.7700 (tt0) REVERT: C 73 ASP cc_start: 0.6747 (t0) cc_final: 0.5894 (p0) outliers start: 10 outliers final: 10 residues processed: 69 average time/residue: 0.1897 time to fit residues: 15.1927 Evaluate side-chains 73 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 28 optimal weight: 0.0670 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 2 optimal weight: 0.4980 chunk 29 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 ASN ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.199250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.165212 restraints weight = 3847.367| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 2.85 r_work: 0.3861 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 2815 Z= 0.238 Angle : 1.382 59.163 3789 Z= 0.820 Chirality : 0.046 0.325 392 Planarity : 0.005 0.058 464 Dihedral : 11.871 59.313 476 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.70 % Allowed : 25.19 % Favored : 71.11 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 14.29 % 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: 1.76 (0.49), residues: 327 helix: 2.33 (0.38), residues: 176 sheet: -1.59 (0.67), residues: 56 loop : 0.92 (0.74), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 94 HIS 0.005 0.001 HIS A 84 PHE 0.011 0.001 PHE A 69 TYR 0.011 0.001 TYR C 95 ARG 0.006 0.000 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03779 ( 166) hydrogen bonds : angle 4.17643 ( 465) SS BOND : bond 0.00505 ( 1) SS BOND : angle 0.43349 ( 2) covalent geometry : bond 0.00436 ( 2814) covalent geometry : angle 1.38210 ( 3787) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2167.32 seconds wall clock time: 37 minutes 46.17 seconds (2266.17 seconds total)