Starting phenix.real_space_refine on Tue Feb 13 07:23:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm4_27526/02_2024/8dm4_27526.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm4_27526/02_2024/8dm4_27526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm4_27526/02_2024/8dm4_27526.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm4_27526/02_2024/8dm4_27526.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm4_27526/02_2024/8dm4_27526.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm4_27526/02_2024/8dm4_27526.pdb" } resolution = 2.45 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= 0.017 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 18 5.16 5 C 2563 2.51 5 N 653 2.21 5 O 784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4018 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2096 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 11, 'TRANS': 245} Chain breaks: 3 Chain: "H" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 976 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "L" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 862 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.89, per 1000 atoms: 0.72 Number of scatterers: 4018 At special positions: 0 Unit cell: (101, 61, 97, 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 18 16.00 O 784 8.00 N 653 7.00 C 2563 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 113 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG B 1 " - " ASN A 122 " Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 843.2 milliseconds 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 924 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 10 sheets defined 1.6% alpha, 47.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'H' and resid 47 through 49 No H-bonds generated for 'chain 'H' and resid 47 through 49' Processing helix chain 'H' and resid 106 through 110 removed outlier: 4.019A pdb=" N THR H 110 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 30 removed outlier: 7.905A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.872A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.766A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 22 through 25 removed outlier: 3.711A pdb=" N VAL H 37 " --> pdb=" O LEU H 102 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU H 102 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 29 through 30 removed outlier: 6.409A pdb=" N GLU H 29 " --> pdb=" O THR H 144 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N MET H 53 " --> pdb=" O GLY H 69 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLY H 69 " --> pdb=" O MET H 53 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP H 55 " --> pdb=" O MET H 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 29 through 30 removed outlier: 6.409A pdb=" N GLU H 29 " --> pdb=" O THR H 144 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 121 through 123 Processing sheet with id=AA9, first strand: chain 'L' and resid 24 through 27 Processing sheet with id=AB1, first strand: chain 'L' and resid 30 through 32 removed outlier: 4.284A pdb=" N ASP L 130 " --> pdb=" O SER L 31 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLN L 62 " --> pdb=" O LEU L 71 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N LEU L 71 " --> pdb=" O GLN L 62 " (cutoff:3.500A) 159 hydrogen bonds defined for protein. 399 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.15 Time building geometry restraints manager: 1.59 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: 1249 1.34 - 1.46: 1064 1.46 - 1.58: 1777 1.58 - 1.70: 0 1.70 - 1.82: 27 Bond restraints: 4117 Sorted by residual: bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.94e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.76e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.16e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.43e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.18e+00 ... (remaining 4112 not shown) Histogram of bond angle deviations from ideal: 95.03 - 102.83: 19 102.83 - 110.62: 1269 110.62 - 118.42: 1884 118.42 - 126.22: 2356 126.22 - 134.01: 66 Bond angle restraints: 5594 Sorted by residual: angle pdb=" C ILE A 197 " pdb=" N ASP A 198 " pdb=" CA ASP A 198 " ideal model delta sigma weight residual 121.54 131.93 -10.39 1.91e+00 2.74e-01 2.96e+01 angle pdb=" C LEU A 141 " pdb=" N ASP A 142 " pdb=" CA ASP A 142 " ideal model delta sigma weight residual 122.93 118.21 4.72 1.45e+00 4.76e-01 1.06e+01 angle pdb=" CA CYS A 131 " pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " ideal model delta sigma weight residual 114.40 121.47 -7.07 2.30e+00 1.89e-01 9.45e+00 angle pdb=" CA ASP A 198 " pdb=" CB ASP A 198 " pdb=" CG ASP A 198 " ideal model delta sigma weight residual 112.60 115.65 -3.05 1.00e+00 1.00e+00 9.29e+00 angle pdb=" N THR L 34 " pdb=" CA THR L 34 " pdb=" C THR L 34 " ideal model delta sigma weight residual 110.35 106.53 3.82 1.38e+00 5.25e-01 7.64e+00 ... (remaining 5589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 2302 17.82 - 35.63: 148 35.63 - 53.45: 27 53.45 - 71.27: 13 71.27 - 89.09: 4 Dihedral angle restraints: 2494 sinusoidal: 1051 harmonic: 1443 Sorted by residual: dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 -51.05 -34.95 1 1.00e+01 1.00e-02 1.73e+01 dihedral pdb=" CA VAL H 24 " pdb=" C VAL H 24 " pdb=" N GLU H 25 " pdb=" CA GLU H 25 " ideal model delta harmonic sigma weight residual -180.00 -159.50 -20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA VAL A 90 " pdb=" C VAL A 90 " pdb=" N TYR A 91 " pdb=" CA TYR A 91 " ideal model delta harmonic sigma weight residual 180.00 162.24 17.76 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 2491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 424 0.051 - 0.102: 159 0.102 - 0.152: 44 0.152 - 0.203: 4 0.203 - 0.254: 3 Chirality restraints: 634 Sorted by residual: chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB THR L 56 " pdb=" CA THR L 56 " pdb=" OG1 THR L 56 " pdb=" CG2 THR L 56 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ASP A 198 " pdb=" N ASP A 198 " pdb=" C ASP A 198 " pdb=" CB ASP A 198 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 631 not shown) Planarity restraints: 711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER L 27 " -0.048 5.00e-02 4.00e+02 7.39e-02 8.74e+00 pdb=" N PRO L 28 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO L 28 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO L 28 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 273 " -0.237 9.50e-02 1.11e+02 1.07e-01 7.74e+00 pdb=" NE ARG A 273 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 273 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 273 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 273 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 210 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.57e+00 pdb=" C ILE A 210 " 0.048 2.00e-02 2.50e+03 pdb=" O ILE A 210 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN A 211 " -0.016 2.00e-02 2.50e+03 ... (remaining 708 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 865 2.79 - 3.32: 3144 3.32 - 3.84: 6623 3.84 - 4.37: 7758 4.37 - 4.90: 13925 Nonbonded interactions: 32315 Sorted by model distance: nonbonded pdb=" OG SER L 90 " pdb=" OG1 THR L 97 " model vdw 2.259 2.440 nonbonded pdb=" OD1 ASP H 109 " pdb=" OH TYR H 113 " model vdw 2.279 2.440 nonbonded pdb=" O SER L 45 " pdb=" OG1 THR L 94 " model vdw 2.307 2.440 nonbonded pdb=" OG SER A 247 " pdb=" OH TYR H 46 " model vdw 2.365 2.440 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.368 2.440 ... (remaining 32310 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 7.430 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: 13.140 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 16.450 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 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 0.045 4117 Z= 0.383 Angle : 0.904 10.390 5594 Z= 0.484 Chirality : 0.057 0.254 634 Planarity : 0.008 0.107 706 Dihedral : 13.358 89.087 1558 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.23 % Allowed : 0.92 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.05 (0.37), residues: 485 helix: None (None), residues: 0 sheet: 0.55 (0.34), residues: 230 loop : -0.55 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP H 66 HIS 0.003 0.001 HIS A 69 PHE 0.025 0.003 PHE A 175 TYR 0.032 0.003 TYR A 145 ARG 0.016 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 0.490 Fit side-chains REVERT: A 80 ASP cc_start: 0.6299 (t0) cc_final: 0.6086 (t0) REVERT: A 100 ILE cc_start: 0.8408 (mp) cc_final: 0.8064 (tp) REVERT: H 52 SER cc_start: 0.7982 (m) cc_final: 0.7705 (p) REVERT: H 65 GLU cc_start: 0.6701 (pt0) cc_final: 0.6168 (pm20) REVERT: H 107 SER cc_start: 0.7089 (m) cc_final: 0.6425 (t) REVERT: H 131 TYR cc_start: 0.8106 (t80) cc_final: 0.7868 (t80) REVERT: H 134 MET cc_start: 0.8612 (mtm) cc_final: 0.8405 (mpp) outliers start: 1 outliers final: 0 residues processed: 100 average time/residue: 1.0437 time to fit residues: 108.3468 Evaluate side-chains 72 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN L 55 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4117 Z= 0.240 Angle : 0.596 8.372 5594 Z= 0.309 Chirality : 0.045 0.214 634 Planarity : 0.005 0.055 706 Dihedral : 7.642 57.883 665 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.75 % Allowed : 10.30 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.29 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.80 (0.35), residues: 215 loop : -0.27 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 66 HIS 0.002 0.001 HIS A 245 PHE 0.019 0.002 PHE A 175 TYR 0.015 0.002 TYR A 28 ARG 0.005 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 0.426 Fit side-chains REVERT: A 80 ASP cc_start: 0.6238 (t0) cc_final: 0.5977 (t0) REVERT: A 169 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7012 (tm-30) REVERT: A 173 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7931 (mp10) REVERT: H 100 MET cc_start: 0.7009 (OUTLIER) cc_final: 0.6716 (ttp) REVERT: H 134 MET cc_start: 0.8624 (mtm) cc_final: 0.8293 (mpp) REVERT: L 132 LYS cc_start: 0.7558 (mmmm) cc_final: 0.7318 (mmmm) outliers start: 12 outliers final: 5 residues processed: 72 average time/residue: 1.2888 time to fit residues: 95.8530 Evaluate side-chains 70 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 62 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 0.0770 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 38 optimal weight: 0.0170 chunk 14 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 32 optimal weight: 0.4980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN L 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4117 Z= 0.167 Angle : 0.542 5.856 5594 Z= 0.285 Chirality : 0.044 0.195 634 Planarity : 0.004 0.047 706 Dihedral : 7.049 57.829 665 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.75 % Allowed : 13.04 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.39 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.81 (0.35), residues: 215 loop : -0.14 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 66 HIS 0.002 0.001 HIS A 69 PHE 0.013 0.001 PHE A 175 TYR 0.012 0.001 TYR A 28 ARG 0.002 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 0.463 Fit side-chains REVERT: A 14 GLN cc_start: 0.7375 (mt0) cc_final: 0.7166 (mt0) REVERT: A 80 ASP cc_start: 0.6222 (t0) cc_final: 0.5976 (t0) REVERT: A 169 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.6982 (tm-30) REVERT: A 177 MET cc_start: 0.7947 (pmt) cc_final: 0.7681 (pmt) REVERT: A 281 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7336 (pt0) REVERT: H 78 MET cc_start: 0.6644 (tpp) cc_final: 0.5898 (tpt) REVERT: H 100 MET cc_start: 0.7025 (OUTLIER) cc_final: 0.6758 (tmm) REVERT: H 109 ASP cc_start: 0.7469 (t0) cc_final: 0.7193 (t0) REVERT: H 134 MET cc_start: 0.8584 (mtm) cc_final: 0.8374 (mpp) REVERT: L 47 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.6873 (tt0) REVERT: L 132 LYS cc_start: 0.7555 (mmmm) cc_final: 0.7258 (mmmm) outliers start: 12 outliers final: 4 residues processed: 71 average time/residue: 1.2554 time to fit residues: 92.2298 Evaluate side-chains 73 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 47 GLN Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 26 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS L 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4117 Z= 0.253 Angle : 0.566 5.982 5594 Z= 0.297 Chirality : 0.045 0.200 634 Planarity : 0.004 0.043 706 Dihedral : 6.710 55.914 665 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.97 % Allowed : 14.19 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.89 (0.35), residues: 214 loop : -0.12 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 66 HIS 0.003 0.001 HIS A 69 PHE 0.021 0.002 PHE A 175 TYR 0.013 0.002 TYR A 28 ARG 0.005 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 0.479 Fit side-chains REVERT: A 14 GLN cc_start: 0.7378 (mt0) cc_final: 0.7148 (mt0) REVERT: A 80 ASP cc_start: 0.6316 (t0) cc_final: 0.6097 (t0) REVERT: A 169 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7000 (tm-30) REVERT: A 173 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7904 (mp10) REVERT: A 177 MET cc_start: 0.7865 (pmt) cc_final: 0.7591 (pmt) REVERT: H 78 MET cc_start: 0.6636 (tpp) cc_final: 0.5895 (tpt) REVERT: H 100 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.7111 (ttp) REVERT: H 134 MET cc_start: 0.8589 (mtm) cc_final: 0.8354 (mpp) outliers start: 13 outliers final: 5 residues processed: 66 average time/residue: 1.2247 time to fit residues: 83.7748 Evaluate side-chains 68 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 41 optimal weight: 0.0020 chunk 11 optimal weight: 0.3980 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN L 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4117 Z= 0.199 Angle : 0.537 5.218 5594 Z= 0.283 Chirality : 0.044 0.194 634 Planarity : 0.004 0.041 706 Dihedral : 6.334 53.127 665 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.29 % Allowed : 15.33 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.53 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.97 (0.35), residues: 212 loop : -0.10 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 66 HIS 0.003 0.001 HIS A 69 PHE 0.016 0.001 PHE A 175 TYR 0.011 0.001 TYR A 28 ARG 0.005 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 0.485 Fit side-chains REVERT: A 80 ASP cc_start: 0.6263 (t0) cc_final: 0.6020 (t0) REVERT: A 169 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.6999 (tm-30) REVERT: A 177 MET cc_start: 0.7839 (pmt) cc_final: 0.7580 (pmt) REVERT: H 78 MET cc_start: 0.6640 (tpp) cc_final: 0.5903 (tpt) REVERT: H 100 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.7105 (ttp) REVERT: L 24 MET cc_start: 0.7634 (mmt) cc_final: 0.6686 (mmt) outliers start: 10 outliers final: 4 residues processed: 68 average time/residue: 1.2324 time to fit residues: 86.8681 Evaluate side-chains 68 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 38 optimal weight: 0.0040 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN L 55 ASN L 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 4117 Z= 0.286 Angle : 0.586 5.226 5594 Z= 0.314 Chirality : 0.046 0.199 634 Planarity : 0.004 0.040 706 Dihedral : 6.293 50.879 665 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.52 % Allowed : 16.93 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.50 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.90 (0.34), residues: 220 loop : -0.10 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 66 HIS 0.003 0.001 HIS A 69 PHE 0.023 0.002 PHE A 175 TYR 0.016 0.002 TYR H 99 ARG 0.007 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 0.517 Fit side-chains REVERT: A 80 ASP cc_start: 0.6236 (t0) cc_final: 0.5990 (t0) REVERT: A 169 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7025 (tm-30) REVERT: A 173 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7883 (mp10) REVERT: A 177 MET cc_start: 0.7826 (pmt) cc_final: 0.7530 (pmt) REVERT: H 100 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.7218 (ttp) outliers start: 11 outliers final: 5 residues processed: 68 average time/residue: 1.2040 time to fit residues: 84.9293 Evaluate side-chains 70 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 62 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 0.1980 chunk 27 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 58 GLN L 55 ASN L 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4117 Z= 0.307 Angle : 0.599 5.329 5594 Z= 0.316 Chirality : 0.047 0.199 634 Planarity : 0.004 0.040 706 Dihedral : 6.163 50.946 665 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.97 % Allowed : 17.85 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.45 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.86 (0.34), residues: 220 loop : -0.13 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 66 HIS 0.003 0.001 HIS A 69 PHE 0.024 0.002 PHE A 175 TYR 0.025 0.002 TYR H 99 ARG 0.007 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 0.470 Fit side-chains REVERT: A 80 ASP cc_start: 0.6218 (t0) cc_final: 0.5978 (t0) REVERT: A 169 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7025 (tm-30) REVERT: A 173 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7889 (mp10) REVERT: A 177 MET cc_start: 0.7818 (pmt) cc_final: 0.7542 (pmt) REVERT: A 202 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8773 (mttm) REVERT: H 100 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.7403 (ttp) REVERT: L 24 MET cc_start: 0.7386 (mmt) cc_final: 0.6725 (mmt) outliers start: 13 outliers final: 6 residues processed: 70 average time/residue: 1.1841 time to fit residues: 85.9145 Evaluate side-chains 70 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 43 optimal weight: 0.0870 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 0.0770 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 58 GLN L 55 ASN L 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4117 Z= 0.205 Angle : 0.555 4.692 5594 Z= 0.294 Chirality : 0.045 0.186 634 Planarity : 0.004 0.039 706 Dihedral : 5.780 51.350 665 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.75 % Allowed : 18.99 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.49 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.89 (0.34), residues: 220 loop : -0.12 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 66 HIS 0.003 0.001 HIS A 69 PHE 0.016 0.001 PHE A 175 TYR 0.022 0.001 TYR H 99 ARG 0.006 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 63 time to evaluate : 0.350 Fit side-chains REVERT: A 80 ASP cc_start: 0.6239 (t0) cc_final: 0.5994 (t0) REVERT: A 131 CYS cc_start: 0.7225 (OUTLIER) cc_final: 0.6672 (m) REVERT: A 169 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.6992 (tm-30) REVERT: A 173 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7861 (mp10) REVERT: H 100 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.7252 (ttp) REVERT: L 24 MET cc_start: 0.7393 (mmt) cc_final: 0.6879 (mmt) outliers start: 12 outliers final: 4 residues processed: 68 average time/residue: 1.0273 time to fit residues: 72.3611 Evaluate side-chains 69 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 42 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 0.0370 overall best weight: 1.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 58 GLN L 55 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4117 Z= 0.338 Angle : 0.613 5.817 5594 Z= 0.322 Chirality : 0.047 0.200 634 Planarity : 0.004 0.039 706 Dihedral : 5.931 50.464 665 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.29 % Allowed : 19.22 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.42 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.92 (0.34), residues: 214 loop : -0.21 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 66 HIS 0.003 0.001 HIS A 69 PHE 0.025 0.002 PHE A 175 TYR 0.021 0.002 TYR H 99 ARG 0.004 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 0.469 Fit side-chains REVERT: A 80 ASP cc_start: 0.6300 (t0) cc_final: 0.6038 (t0) REVERT: A 169 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7032 (tm-30) REVERT: A 173 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7895 (mp10) REVERT: H 100 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7475 (ttp) REVERT: L 24 MET cc_start: 0.7280 (mmt) cc_final: 0.6315 (mmt) outliers start: 10 outliers final: 5 residues processed: 65 average time/residue: 1.1864 time to fit residues: 79.9511 Evaluate side-chains 67 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 59 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 30 optimal weight: 0.4980 chunk 40 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 58 GLN L 55 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 4117 Z= 0.230 Angle : 0.570 4.801 5594 Z= 0.303 Chirality : 0.045 0.174 634 Planarity : 0.004 0.039 706 Dihedral : 5.911 51.234 665 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.06 % Allowed : 19.68 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.36 (0.37), residues: 485 helix: None (None), residues: 0 sheet: 0.89 (0.34), residues: 214 loop : -0.27 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 66 HIS 0.003 0.001 HIS A 69 PHE 0.018 0.002 PHE A 175 TYR 0.021 0.002 TYR H 99 ARG 0.004 0.000 ARG A 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 0.482 Fit side-chains REVERT: A 80 ASP cc_start: 0.6281 (t0) cc_final: 0.6029 (t0) REVERT: A 169 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7029 (tm-30) REVERT: A 173 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7843 (mp10) REVERT: H 53 MET cc_start: 0.7689 (tpp) cc_final: 0.7348 (tpt) REVERT: H 100 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.7313 (ttp) REVERT: L 24 MET cc_start: 0.7116 (mmt) cc_final: 0.6521 (mmt) outliers start: 9 outliers final: 5 residues processed: 66 average time/residue: 1.1970 time to fit residues: 81.8860 Evaluate side-chains 68 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 0.0000 chunk 25 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 58 GLN L 55 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.141570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.098253 restraints weight = 5560.718| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.20 r_work: 0.3180 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 4117 Z= 0.314 Angle : 0.614 6.080 5594 Z= 0.325 Chirality : 0.047 0.174 634 Planarity : 0.004 0.039 706 Dihedral : 5.983 50.537 665 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.06 % Allowed : 19.68 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 (0.37), residues: 485 helix: None (None), residues: 0 sheet: 0.84 (0.34), residues: 214 loop : -0.41 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 66 HIS 0.003 0.001 HIS A 69 PHE 0.024 0.002 PHE A 175 TYR 0.021 0.002 TYR H 99 ARG 0.004 0.001 ARG A 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2375.98 seconds wall clock time: 42 minutes 42.46 seconds (2562.46 seconds total)