Starting phenix.real_space_refine on Wed Nov 13 23:35:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j46_35971/11_2024/8j46_35971_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j46_35971/11_2024/8j46_35971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j46_35971/11_2024/8j46_35971.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j46_35971/11_2024/8j46_35971.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j46_35971/11_2024/8j46_35971_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j46_35971/11_2024/8j46_35971_neut.cif" } resolution = 3.66 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= 0.010 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 4 5.16 5 C 1381 2.51 5 N 383 2.21 5 O 390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 2158 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2158 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 204} Link IDs: {'PTRANS': 14, 'TRANS': 347} Chain breaks: 5 Unresolved non-hydrogen bonds: 733 Unresolved non-hydrogen angles: 931 Unresolved non-hydrogen dihedrals: 601 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 12, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 3, 'HIS:plan': 5, 'PHE:plan': 10, 'GLU:plan': 12, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 340 Time building chain proxies: 2.44, per 1000 atoms: 1.13 Number of scatterers: 2158 At special positions: 0 Unit cell: (60.208, 80.56, 109.392, 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 4 16.00 O 390 8.00 N 383 7.00 C 1381 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 181 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 347.5 milliseconds 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 696 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 1 sheets defined 87.3% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 29 through 52 removed outlier: 4.342A pdb=" N PHE A 33 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 77 Processing helix chain 'A' and resid 79 through 90 removed outlier: 3.637A pdb=" N MET A 83 " --> pdb=" O THR A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 130 Processing helix chain 'A' and resid 133 through 138 Processing helix chain 'A' and resid 139 through 159 Processing helix chain 'A' and resid 159 through 168 removed outlier: 4.118A pdb=" N PHE A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 188 removed outlier: 3.673A pdb=" N LYS A 188 " --> pdb=" O MET A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 209 removed outlier: 3.820A pdb=" N TYR A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 1019 removed outlier: 3.634A pdb=" N ILE A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA A 996 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG A 997 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG A 998 " --> pdb=" O ARG A 225 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A1003 " --> pdb=" O GLN A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1044 removed outlier: 3.567A pdb=" N LYS A1032 " --> pdb=" O ASP A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1081 removed outlier: 3.632A pdb=" N ASP A1066 " --> pdb=" O ARG A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 242 removed outlier: 3.855A pdb=" N ALA A1087 " --> pdb=" O LYS A1083 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR A1096 " --> pdb=" O GLU A1092 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR A1097 " --> pdb=" O GLN A1093 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN A1103 " --> pdb=" O ASN A1099 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LYS A1104 " --> pdb=" O ALA A1100 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A1110 " --> pdb=" O LEU A1106 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER A1111 " --> pdb=" O GLU A1107 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 237 " --> pdb=" O ARG A1110 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A 238 " --> pdb=" O SER A1111 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA A 239 " --> pdb=" O THR A1112 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU A 240 " --> pdb=" O LEU A1113 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 264 removed outlier: 3.641A pdb=" N ILE A 247 " --> pdb=" O CYS A 243 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Proline residue: A 256 - end of helix Processing helix chain 'A' and resid 271 through 294 removed outlier: 3.586A pdb=" N HIS A 275 " --> pdb=" O PRO A 271 " (cutoff:3.500A) Proline residue: A 286 - end of helix Proline residue: A 291 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 95 removed outlier: 8.868A pdb=" N ILE A 176 " --> pdb=" O SER A 13 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LEU A 15 " --> pdb=" O ILE A 176 " (cutoff:3.500A) 216 hydrogen bonds defined for protein. 648 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: 0.61 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 643 1.33 - 1.45: 278 1.45 - 1.57: 1269 1.57 - 1.69: 0 1.69 - 1.80: 4 Bond restraints: 2194 Sorted by residual: bond pdb=" N PRO A 11 " pdb=" CD PRO A 11 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.55e+01 bond pdb=" C MET A 112 " pdb=" O MET A 112 " ideal model delta sigma weight residual 1.237 1.218 0.019 1.19e-02 7.06e+03 2.48e+00 bond pdb=" N HIS A1063 " pdb=" CA HIS A1063 " ideal model delta sigma weight residual 1.459 1.441 0.018 1.21e-02 6.83e+03 2.18e+00 bond pdb=" C MET A 112 " pdb=" N GLU A 113 " ideal model delta sigma weight residual 1.335 1.316 0.019 1.31e-02 5.83e+03 2.13e+00 bond pdb=" C LEU A 156 " pdb=" O LEU A 156 " ideal model delta sigma weight residual 1.237 1.220 0.017 1.17e-02 7.31e+03 2.01e+00 ... (remaining 2189 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 2902 1.51 - 3.02: 102 3.02 - 4.53: 19 4.53 - 6.04: 14 6.04 - 7.55: 3 Bond angle restraints: 3040 Sorted by residual: angle pdb=" N ALA A 226 " pdb=" CA ALA A 226 " pdb=" C ALA A 226 " ideal model delta sigma weight residual 111.36 117.35 -5.99 1.09e+00 8.42e-01 3.02e+01 angle pdb=" N THR A1112 " pdb=" CA THR A1112 " pdb=" C THR A1112 " ideal model delta sigma weight residual 111.36 117.21 -5.85 1.09e+00 8.42e-01 2.88e+01 angle pdb=" N LEU A 237 " pdb=" CA LEU A 237 " pdb=" C LEU A 237 " ideal model delta sigma weight residual 111.28 116.26 -4.98 1.09e+00 8.42e-01 2.09e+01 angle pdb=" N LYS A1015 " pdb=" CA LYS A1015 " pdb=" C LYS A1015 " ideal model delta sigma weight residual 111.28 106.42 4.86 1.09e+00 8.42e-01 1.99e+01 angle pdb=" N ASN A1022 " pdb=" CA ASN A1022 " pdb=" C ASN A1022 " ideal model delta sigma weight residual 109.24 115.74 -6.50 1.51e+00 4.39e-01 1.86e+01 ... (remaining 3035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.19: 1176 9.19 - 18.37: 51 18.37 - 27.56: 25 27.56 - 36.74: 19 36.74 - 45.93: 4 Dihedral angle restraints: 1275 sinusoidal: 213 harmonic: 1062 Sorted by residual: dihedral pdb=" CB CYS A 99 " pdb=" SG CYS A 99 " pdb=" SG CYS A 181 " pdb=" CB CYS A 181 " ideal model delta sinusoidal sigma weight residual -86.00 -118.25 32.25 1 1.00e+01 1.00e-02 1.48e+01 dihedral pdb=" CA LEU A 164 " pdb=" CB LEU A 164 " pdb=" CG LEU A 164 " pdb=" CD1 LEU A 164 " ideal model delta sinusoidal sigma weight residual 180.00 137.88 42.12 3 1.50e+01 4.44e-03 7.55e+00 dihedral pdb=" N LEU A1038 " pdb=" CA LEU A1038 " pdb=" CB LEU A1038 " pdb=" CG LEU A1038 " ideal model delta sinusoidal sigma weight residual -60.00 -101.23 41.23 3 1.50e+01 4.44e-03 7.37e+00 ... (remaining 1272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 326 0.061 - 0.122: 56 0.122 - 0.183: 9 0.183 - 0.244: 2 0.244 - 0.305: 1 Chirality restraints: 394 Sorted by residual: chirality pdb=" CA TYR A1101 " pdb=" N TYR A1101 " pdb=" C TYR A1101 " pdb=" CB TYR A1101 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA ASP A1021 " pdb=" N ASP A1021 " pdb=" C ASP A1021 " pdb=" CB ASP A1021 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA ALA A 226 " pdb=" N ALA A 226 " pdb=" C ALA A 226 " pdb=" CB ALA A 226 " both_signs ideal model delta sigma weight residual False 2.48 2.29 0.20 2.00e-01 2.50e+01 9.58e-01 ... (remaining 391 not shown) Planarity restraints: 406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 225 " -0.017 2.00e-02 2.50e+03 3.44e-02 1.19e+01 pdb=" C ARG A 225 " 0.060 2.00e-02 2.50e+03 pdb=" O ARG A 225 " -0.023 2.00e-02 2.50e+03 pdb=" N ALA A 226 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 159 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.62e+00 pdb=" N PRO A 160 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 160 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 160 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 286 " 0.037 5.00e-02 4.00e+02 5.59e-02 5.00e+00 pdb=" N PRO A 287 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 287 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 287 " 0.032 5.00e-02 4.00e+02 ... (remaining 403 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 1006 2.95 - 3.44: 2404 3.44 - 3.93: 3253 3.93 - 4.41: 3225 4.41 - 4.90: 5483 Nonbonded interactions: 15371 Sorted by model distance: nonbonded pdb=" O THR A 135 " pdb=" O LEU A 138 " model vdw 2.463 3.040 nonbonded pdb=" ND2 ASN A 44 " pdb=" OD2 ASP A 72 " model vdw 2.506 3.120 nonbonded pdb=" O ASP A1005 " pdb=" OD1 ASP A1005 " model vdw 2.554 3.040 nonbonded pdb=" O ASN A1013 " pdb=" OD1 ASN A1013 " model vdw 2.563 3.040 nonbonded pdb=" O VAL A1016 " pdb=" O LYS A1019 " model vdw 2.577 3.040 ... (remaining 15366 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.620 Find NCS groups from input model: 0.020 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 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 : 0.004 0.055 2194 Z= 0.258 Angle : 0.772 7.551 3040 Z= 0.525 Chirality : 0.052 0.305 394 Planarity : 0.006 0.059 406 Dihedral : 9.516 45.928 576 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 0.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 0.00 % Allowed : 16.35 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.46), residues: 350 helix: 2.46 (0.31), residues: 282 sheet: None (None), residues: 0 loop : -1.28 (0.72), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.003 0.001 HIS A 183 PHE 0.004 0.001 PHE A 161 TYR 0.008 0.001 TYR A 134 ARG 0.001 0.000 ARG A 997 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.240 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0735 time to fit residues: 5.3781 Evaluate side-chains 30 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1006 ASN A 290 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 2194 Z= 0.374 Angle : 0.709 7.400 3040 Z= 0.398 Chirality : 0.045 0.132 394 Planarity : 0.005 0.049 406 Dihedral : 3.872 15.560 367 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.85 % Allowed : 23.08 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.45), residues: 350 helix: 1.75 (0.30), residues: 298 sheet: None (None), residues: 0 loop : -2.77 (0.73), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.013 0.004 HIS A 178 PHE 0.026 0.003 PHE A 87 TYR 0.014 0.002 TYR A 62 ARG 0.004 0.002 ARG A 997 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.263 Fit side-chains REVERT: A 37 TYR cc_start: 0.9016 (t80) cc_final: 0.8720 (t80) outliers start: 4 outliers final: 1 residues processed: 34 average time/residue: 0.0697 time to fit residues: 3.3038 Evaluate side-chains 30 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS A1006 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 2194 Z= 0.160 Angle : 0.537 8.021 3040 Z= 0.273 Chirality : 0.040 0.126 394 Planarity : 0.004 0.047 406 Dihedral : 3.210 11.145 367 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 6.73 % Allowed : 20.19 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.93 (0.46), residues: 350 helix: 2.65 (0.30), residues: 298 sheet: None (None), residues: 0 loop : -2.64 (0.72), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.006 0.002 HIS A 178 PHE 0.010 0.002 PHE A 87 TYR 0.008 0.001 TYR A 125 ARG 0.002 0.001 ARG A 997 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.242 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 37 average time/residue: 0.0711 time to fit residues: 3.6509 Evaluate side-chains 33 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 99 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 0.9980 chunk 3 optimal weight: 20.0000 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2194 Z= 0.203 Angle : 0.533 5.256 3040 Z= 0.282 Chirality : 0.040 0.144 394 Planarity : 0.004 0.042 406 Dihedral : 3.313 12.728 367 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.85 % Allowed : 23.08 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.09 (0.47), residues: 350 helix: 2.67 (0.31), residues: 306 sheet: None (None), residues: 0 loop : -2.93 (0.81), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.005 0.001 HIS A 107 PHE 0.032 0.002 PHE A 87 TYR 0.012 0.001 TYR A 37 ARG 0.001 0.000 ARG A 997 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.317 Fit side-chains REVERT: A 80 ILE cc_start: 0.9403 (mm) cc_final: 0.9147 (tp) outliers start: 4 outliers final: 3 residues processed: 37 average time/residue: 0.0746 time to fit residues: 3.7905 Evaluate side-chains 35 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 1063 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 2194 Z= 0.220 Angle : 0.532 5.051 3040 Z= 0.286 Chirality : 0.040 0.143 394 Planarity : 0.004 0.039 406 Dihedral : 3.383 12.447 367 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 5.77 % Allowed : 27.88 % Favored : 66.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.02 (0.47), residues: 350 helix: 2.69 (0.31), residues: 301 sheet: None (None), residues: 0 loop : -2.83 (0.79), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.005 0.002 HIS A 107 PHE 0.010 0.001 PHE A 104 TYR 0.018 0.001 TYR A 37 ARG 0.001 0.001 ARG A 997 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.245 Fit side-chains REVERT: A 14 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.7146 (m-10) REVERT: A 37 TYR cc_start: 0.8888 (t80) cc_final: 0.8282 (t80) REVERT: A 80 ILE cc_start: 0.9404 (mm) cc_final: 0.9024 (mt) outliers start: 6 outliers final: 3 residues processed: 39 average time/residue: 0.0700 time to fit residues: 3.7264 Evaluate side-chains 39 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 1063 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.0010 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2194 Z= 0.146 Angle : 0.498 6.126 3040 Z= 0.259 Chirality : 0.039 0.153 394 Planarity : 0.004 0.039 406 Dihedral : 3.238 14.730 367 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.88 % Allowed : 30.77 % Favored : 66.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.47 (0.48), residues: 350 helix: 2.97 (0.31), residues: 303 sheet: None (None), residues: 0 loop : -2.78 (0.78), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.003 0.001 HIS A 107 PHE 0.008 0.001 PHE A 87 TYR 0.013 0.001 TYR A 37 ARG 0.000 0.000 ARG A 997 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.246 Fit side-chains REVERT: A 37 TYR cc_start: 0.8829 (t80) cc_final: 0.8213 (t80) REVERT: A 80 ILE cc_start: 0.9364 (mm) cc_final: 0.8983 (mt) outliers start: 3 outliers final: 3 residues processed: 37 average time/residue: 0.0760 time to fit residues: 3.8668 Evaluate side-chains 38 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 1063 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 16 optimal weight: 0.0170 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 overall best weight: 2.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2194 Z= 0.246 Angle : 0.560 5.265 3040 Z= 0.305 Chirality : 0.041 0.155 394 Planarity : 0.004 0.038 406 Dihedral : 3.411 12.006 367 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 5.77 % Allowed : 27.88 % Favored : 66.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.16 (0.47), residues: 350 helix: 2.77 (0.31), residues: 296 sheet: None (None), residues: 0 loop : -2.16 (0.83), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.006 0.002 HIS A 107 PHE 0.016 0.002 PHE A 87 TYR 0.013 0.001 TYR A 37 ARG 0.001 0.001 ARG A 997 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: A 14 PHE cc_start: 0.7912 (OUTLIER) cc_final: 0.7665 (m-80) REVERT: A 37 TYR cc_start: 0.8912 (t80) cc_final: 0.8316 (t80) REVERT: A 80 ILE cc_start: 0.9368 (mm) cc_final: 0.8983 (mt) outliers start: 6 outliers final: 4 residues processed: 39 average time/residue: 0.0727 time to fit residues: 3.9872 Evaluate side-chains 37 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 1063 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 0.0050 chunk 3 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 33 optimal weight: 0.1980 chunk 30 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 2194 Z= 0.155 Angle : 0.496 5.101 3040 Z= 0.262 Chirality : 0.040 0.190 394 Planarity : 0.004 0.040 406 Dihedral : 3.138 10.654 367 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.88 % Allowed : 30.77 % Favored : 66.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.44 (0.47), residues: 350 helix: 2.97 (0.31), residues: 296 sheet: None (None), residues: 0 loop : -2.10 (0.83), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.002 0.001 HIS A 107 PHE 0.038 0.002 PHE A 87 TYR 0.012 0.001 TYR A 37 ARG 0.001 0.000 ARG A 997 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8842 (t80) cc_final: 0.8412 (t80) REVERT: A 80 ILE cc_start: 0.9309 (mm) cc_final: 0.9046 (tp) outliers start: 3 outliers final: 3 residues processed: 39 average time/residue: 0.0733 time to fit residues: 3.9412 Evaluate side-chains 36 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 1063 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2194 Z= 0.247 Angle : 0.546 5.318 3040 Z= 0.295 Chirality : 0.041 0.191 394 Planarity : 0.004 0.039 406 Dihedral : 3.381 10.632 367 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.85 % Allowed : 30.77 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.16 (0.47), residues: 350 helix: 2.76 (0.31), residues: 296 sheet: None (None), residues: 0 loop : -2.04 (0.87), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.006 0.002 HIS A 107 PHE 0.014 0.002 PHE A 87 TYR 0.012 0.002 TYR A 37 ARG 0.001 0.000 ARG A 997 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8903 (t80) cc_final: 0.8647 (t80) REVERT: A 99 CYS cc_start: 0.7391 (m) cc_final: 0.7000 (m) outliers start: 4 outliers final: 4 residues processed: 36 average time/residue: 0.0705 time to fit residues: 3.5484 Evaluate side-chains 38 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 1063 HIS Chi-restraints excluded: chain A residue 293 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 4 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1006 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2194 Z= 0.284 Angle : 0.581 6.006 3040 Z= 0.316 Chirality : 0.042 0.209 394 Planarity : 0.004 0.041 406 Dihedral : 3.646 12.687 367 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.85 % Allowed : 32.69 % Favored : 63.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.77 (0.47), residues: 350 helix: 2.50 (0.30), residues: 295 sheet: None (None), residues: 0 loop : -2.12 (0.85), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.006 0.002 HIS A 107 PHE 0.012 0.002 PHE A 104 TYR 0.014 0.002 TYR A 37 ARG 0.002 0.001 ARG A 997 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8907 (t80) cc_final: 0.8643 (t80) REVERT: A 99 CYS cc_start: 0.7505 (m) cc_final: 0.7159 (m) outliers start: 4 outliers final: 4 residues processed: 36 average time/residue: 0.0718 time to fit residues: 3.6150 Evaluate side-chains 38 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 1063 HIS Chi-restraints excluded: chain A residue 293 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 1 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 32 optimal weight: 0.0570 chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1006 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.075679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.065762 restraints weight = 13816.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.066937 restraints weight = 9105.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.067788 restraints weight = 6721.447| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2194 Z= 0.165 Angle : 0.500 4.924 3040 Z= 0.264 Chirality : 0.040 0.185 394 Planarity : 0.004 0.042 406 Dihedral : 3.267 11.809 367 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.81 % Allowed : 29.81 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.39 (0.47), residues: 350 helix: 2.92 (0.30), residues: 296 sheet: None (None), residues: 0 loop : -2.01 (0.87), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 HIS 0.003 0.001 HIS A 246 PHE 0.010 0.001 PHE A 87 TYR 0.013 0.001 TYR A 37 ARG 0.001 0.000 ARG A 997 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 785.48 seconds wall clock time: 15 minutes 5.99 seconds (905.99 seconds total)