Starting phenix.real_space_refine on Fri Aug 2 15:52:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kb4_37069/08_2024/8kb4_37069_neut_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kb4_37069/08_2024/8kb4_37069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kb4_37069/08_2024/8kb4_37069.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kb4_37069/08_2024/8kb4_37069.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kb4_37069/08_2024/8kb4_37069_neut_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kb4_37069/08_2024/8kb4_37069_neut_trim.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 20 5.16 5 C 2234 2.51 5 N 535 2.21 5 O 577 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 3367 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3293 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 11, 'TRANS': 390} Chain breaks: 2 Chain: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 74 Unusual residues: {'65I': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.94, per 1000 atoms: 0.87 Number of scatterers: 3367 At special positions: 0 Unit cell: (57.664, 66.992, 112.784, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 1 15.00 O 577 8.00 N 535 7.00 C 2234 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 128 " distance=2.03 Simple disulfide: pdb=" SG CYS A 89 " - pdb=" SG CYS A 431 " distance=2.04 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 NAG-ASN " NAG A 901 " - " ASN A 79 " " NAG A 902 " - " ASN A 127 " Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 576.8 milliseconds 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 764 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 2 sheets defined 54.7% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 90 through 95 Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 100 through 110 removed outlier: 4.080A pdb=" N GLU A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 251 Processing helix chain 'A' and resid 256 through 287 removed outlier: 3.501A pdb=" N PHE A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY A 263 " --> pdb=" O GLN A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 318 Processing helix chain 'A' and resid 326 through 331 removed outlier: 4.259A pdb=" N LEU A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 337 Processing helix chain 'A' and resid 338 through 354 removed outlier: 4.198A pdb=" N LEU A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 350 " --> pdb=" O MET A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 393 removed outlier: 4.277A pdb=" N LEU A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 427 removed outlier: 3.643A pdb=" N SER A 399 " --> pdb=" O ILE A 395 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU A 400 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 442 Processing helix chain 'A' and resid 443 through 460 Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 44 removed outlier: 3.713A pdb=" N ASP A 70 " --> pdb=" O THR A 207 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 59 removed outlier: 3.974A pdb=" N SER A 77 " --> pdb=" O SER A 191 " (cutoff:3.500A) 197 hydrogen bonds defined for protein. 576 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: 0.79 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 493 1.31 - 1.43: 1013 1.43 - 1.56: 1913 1.56 - 1.69: 2 1.69 - 1.81: 33 Bond restraints: 3454 Sorted by residual: bond pdb=" C11 65I A 903 " pdb=" O6 65I A 903 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C5 65I A 903 " pdb=" O1 65I A 903 " ideal model delta sigma weight residual 1.335 1.400 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" C1 NAG A 902 " pdb=" O5 NAG A 902 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.81e+00 bond pdb=" C7 65I A 903 " pdb=" O6 65I A 903 " ideal model delta sigma weight residual 1.429 1.399 0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" C6 65I A 903 " pdb=" O1 65I A 903 " ideal model delta sigma weight residual 1.427 1.399 0.028 2.00e-02 2.50e+03 1.95e+00 ... (remaining 3449 not shown) Histogram of bond angle deviations from ideal: 100.42 - 107.50: 115 107.50 - 114.58: 2057 114.58 - 121.66: 1795 121.66 - 128.73: 674 128.73 - 135.81: 36 Bond angle restraints: 4677 Sorted by residual: angle pdb=" C17 65I A 903 " pdb=" C18 65I A 903 " pdb=" C19 65I A 903 " ideal model delta sigma weight residual 114.14 135.81 -21.67 3.00e+00 1.11e-01 5.22e+01 angle pdb=" C THR A 357 " pdb=" N ASP A 358 " pdb=" CA ASP A 358 " ideal model delta sigma weight residual 122.61 130.38 -7.77 1.56e+00 4.11e-01 2.48e+01 angle pdb=" O3 65I A 903 " pdb=" P 65I A 903 " pdb=" O4 65I A 903 " ideal model delta sigma weight residual 122.02 109.40 12.62 3.00e+00 1.11e-01 1.77e+01 angle pdb=" O2 65I A 903 " pdb=" P 65I A 903 " pdb=" O5 65I A 903 " ideal model delta sigma weight residual 98.05 109.63 -11.58 3.00e+00 1.11e-01 1.49e+01 angle pdb=" N ASP A 75 " pdb=" CA ASP A 75 " pdb=" C ASP A 75 " ideal model delta sigma weight residual 113.18 108.39 4.79 1.33e+00 5.65e-01 1.30e+01 ... (remaining 4672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.61: 1924 25.61 - 51.22: 112 51.22 - 76.82: 18 76.82 - 102.43: 9 102.43 - 128.04: 6 Dihedral angle restraints: 2069 sinusoidal: 889 harmonic: 1180 Sorted by residual: dihedral pdb=" CB CYS A 74 " pdb=" SG CYS A 74 " pdb=" SG CYS A 128 " pdb=" CB CYS A 128 " ideal model delta sinusoidal sigma weight residual -86.00 -37.98 -48.02 1 1.00e+01 1.00e-02 3.18e+01 dihedral pdb=" C2 65I A 903 " pdb=" C3 65I A 903 " pdb=" C4 65I A 903 " pdb=" C5 65I A 903 " ideal model delta sinusoidal sigma weight residual -173.23 -45.19 -128.04 1 3.00e+01 1.11e-03 1.72e+01 dihedral pdb=" C2 NAG A 902 " pdb=" C1 NAG A 902 " pdb=" O5 NAG A 902 " pdb=" C5 NAG A 902 " ideal model delta sinusoidal sigma weight residual -62.96 60.58 -123.54 1 3.00e+01 1.11e-03 1.66e+01 ... (remaining 2066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 361 0.031 - 0.062: 127 0.062 - 0.092: 32 0.092 - 0.123: 10 0.123 - 0.154: 5 Chirality restraints: 535 Sorted by residual: chirality pdb=" C1 NAG A 902 " pdb=" ND2 ASN A 127 " pdb=" C2 NAG A 902 " pdb=" O5 NAG A 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CA ILE A 183 " pdb=" N ILE A 183 " pdb=" C ILE A 183 " pdb=" CB ILE A 183 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA ASP A 358 " pdb=" N ASP A 358 " pdb=" C ASP A 358 " pdb=" CB ASP A 358 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 532 not shown) Planarity restraints: 557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 72 " -0.031 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO A 73 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 73 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 73 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 357 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C THR A 357 " 0.029 2.00e-02 2.50e+03 pdb=" O THR A 357 " -0.011 2.00e-02 2.50e+03 pdb=" N ASP A 358 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 221 " -0.005 2.00e-02 2.50e+03 9.91e-03 9.81e-01 pdb=" C LEU A 221 " 0.017 2.00e-02 2.50e+03 pdb=" O LEU A 221 " -0.006 2.00e-02 2.50e+03 pdb=" N GLU A 222 " -0.006 2.00e-02 2.50e+03 ... (remaining 554 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 77 2.70 - 3.25: 3391 3.25 - 3.80: 5040 3.80 - 4.35: 5860 4.35 - 4.90: 10338 Nonbonded interactions: 24706 Sorted by model distance: nonbonded pdb=" N GLU A 217 " pdb=" OE1 GLU A 217 " model vdw 2.151 3.120 nonbonded pdb=" O THR A 357 " pdb=" OD1 ASP A 358 " model vdw 2.207 3.040 nonbonded pdb=" N GLY A 71 " pdb=" OE2 GLU A 130 " model vdw 2.231 3.120 nonbonded pdb=" O GLN A 178 " pdb=" OH TYR A 182 " model vdw 2.256 3.040 nonbonded pdb=" OD1 ASN A 91 " pdb=" N GLU A 92 " model vdw 2.266 3.120 ... (remaining 24701 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: 0.930 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.360 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 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 0.069 3454 Z= 0.271 Angle : 0.703 21.673 4677 Z= 0.323 Chirality : 0.037 0.154 535 Planarity : 0.003 0.048 555 Dihedral : 19.096 128.040 1299 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: 1.68 (0.47), residues: 396 helix: 3.28 (0.38), residues: 204 sheet: 0.04 (0.68), residues: 67 loop : -2.19 (0.54), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 247 HIS 0.002 0.001 HIS A 171 PHE 0.010 0.001 PHE A 379 TYR 0.009 0.001 TYR A 104 ARG 0.001 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 434 ASP cc_start: 0.8624 (p0) cc_final: 0.8414 (p0) REVERT: A 465 ASN cc_start: 0.9337 (t0) cc_final: 0.9035 (t0) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1207 time to fit residues: 7.5698 Evaluate side-chains 40 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3454 Z= 0.206 Angle : 0.606 6.500 4677 Z= 0.306 Chirality : 0.040 0.174 535 Planarity : 0.005 0.064 555 Dihedral : 17.369 109.370 533 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.56 % Allowed : 5.32 % Favored : 94.12 % 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: 2.12 (0.47), residues: 396 helix: 3.69 (0.37), residues: 204 sheet: 0.61 (0.69), residues: 63 loop : -2.24 (0.53), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 247 HIS 0.003 0.001 HIS A 171 PHE 0.013 0.001 PHE A 55 TYR 0.016 0.002 TYR A 340 ARG 0.003 0.001 ARG A 351 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 465 ASN cc_start: 0.9288 (t0) cc_final: 0.8977 (t0) outliers start: 2 outliers final: 1 residues processed: 40 average time/residue: 0.1425 time to fit residues: 7.4124 Evaluate side-chains 34 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 0.0020 chunk 35 optimal weight: 0.0570 chunk 27 optimal weight: 2.9990 chunk 18 optimal weight: 0.0870 overall best weight: 0.4086 ------------------------------------------------------------------------------- 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: 0.8136 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3454 Z= 0.146 Angle : 0.555 7.643 4677 Z= 0.273 Chirality : 0.039 0.162 535 Planarity : 0.004 0.064 555 Dihedral : 14.610 102.604 533 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.28 % Allowed : 10.08 % Favored : 89.64 % 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: 2.22 (0.46), residues: 396 helix: 3.76 (0.37), residues: 206 sheet: 0.69 (0.67), residues: 63 loop : -2.30 (0.52), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 42 HIS 0.002 0.001 HIS A 171 PHE 0.010 0.001 PHE A 55 TYR 0.012 0.001 TYR A 90 ARG 0.003 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.406 Fit side-chains REVERT: A 308 MET cc_start: 0.8813 (tpt) cc_final: 0.8430 (tpt) REVERT: A 442 ASP cc_start: 0.8382 (m-30) cc_final: 0.8025 (m-30) REVERT: A 465 ASN cc_start: 0.9303 (t0) cc_final: 0.9001 (t0) outliers start: 1 outliers final: 1 residues processed: 37 average time/residue: 0.1255 time to fit residues: 6.3024 Evaluate side-chains 35 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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: 0.8236 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3454 Z= 0.325 Angle : 0.630 9.748 4677 Z= 0.308 Chirality : 0.041 0.216 535 Planarity : 0.005 0.064 555 Dihedral : 13.793 99.791 533 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.68 % Allowed : 11.48 % Favored : 86.83 % 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: 1.98 (0.45), residues: 396 helix: 3.50 (0.36), residues: 206 sheet: 0.77 (0.67), residues: 63 loop : -2.43 (0.50), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 252 HIS 0.003 0.001 HIS A 187 PHE 0.016 0.001 PHE A 55 TYR 0.011 0.001 TYR A 340 ARG 0.002 0.000 ARG A 436 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 141 PHE cc_start: 0.7764 (m-80) cc_final: 0.7427 (m-80) REVERT: A 442 ASP cc_start: 0.8372 (m-30) cc_final: 0.8035 (m-30) REVERT: A 465 ASN cc_start: 0.9322 (t0) cc_final: 0.8986 (t0) outliers start: 6 outliers final: 4 residues processed: 37 average time/residue: 0.1219 time to fit residues: 6.0242 Evaluate side-chains 37 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 33 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 7.9990 chunk 15 optimal weight: 0.0000 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- 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: 0.8174 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3454 Z= 0.169 Angle : 0.552 7.909 4677 Z= 0.269 Chirality : 0.039 0.166 535 Planarity : 0.004 0.063 555 Dihedral : 12.813 92.265 533 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.84 % Allowed : 13.17 % Favored : 85.99 % 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: 2.17 (0.46), residues: 396 helix: 3.70 (0.37), residues: 206 sheet: 0.78 (0.67), residues: 63 loop : -2.35 (0.51), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 82 HIS 0.001 0.001 HIS A 187 PHE 0.011 0.001 PHE A 55 TYR 0.011 0.001 TYR A 340 ARG 0.002 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 141 PHE cc_start: 0.7810 (m-80) cc_final: 0.7531 (m-80) REVERT: A 465 ASN cc_start: 0.9322 (t0) cc_final: 0.8988 (t0) outliers start: 3 outliers final: 1 residues processed: 37 average time/residue: 0.1217 time to fit residues: 6.1148 Evaluate side-chains 36 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8178 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3454 Z= 0.178 Angle : 0.555 7.712 4677 Z= 0.272 Chirality : 0.038 0.172 535 Planarity : 0.004 0.063 555 Dihedral : 12.202 90.154 533 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.40 % Allowed : 13.45 % Favored : 85.15 % 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: 2.20 (0.46), residues: 396 helix: 3.73 (0.36), residues: 206 sheet: 0.80 (0.68), residues: 63 loop : -2.36 (0.51), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 82 HIS 0.001 0.001 HIS A 187 PHE 0.011 0.001 PHE A 55 TYR 0.011 0.001 TYR A 340 ARG 0.001 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.320 Fit side-chains REVERT: A 141 PHE cc_start: 0.7859 (m-80) cc_final: 0.7579 (m-80) REVERT: A 442 ASP cc_start: 0.8394 (m-30) cc_final: 0.8051 (m-30) REVERT: A 465 ASN cc_start: 0.9316 (t0) cc_final: 0.8974 (t0) outliers start: 5 outliers final: 4 residues processed: 40 average time/residue: 0.1523 time to fit residues: 7.8492 Evaluate side-chains 38 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 34 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.8190 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3454 Z= 0.201 Angle : 0.549 7.441 4677 Z= 0.271 Chirality : 0.039 0.180 535 Planarity : 0.004 0.062 555 Dihedral : 11.683 87.879 533 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.40 % Allowed : 14.57 % Favored : 84.03 % 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: 2.16 (0.46), residues: 396 helix: 3.68 (0.36), residues: 206 sheet: 0.86 (0.67), residues: 63 loop : -2.39 (0.50), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 82 HIS 0.002 0.001 HIS A 171 PHE 0.013 0.001 PHE A 55 TYR 0.010 0.001 TYR A 340 ARG 0.001 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.386 Fit side-chains REVERT: A 141 PHE cc_start: 0.7908 (m-80) cc_final: 0.7609 (m-80) REVERT: A 441 ASP cc_start: 0.8241 (p0) cc_final: 0.7758 (p0) REVERT: A 442 ASP cc_start: 0.8332 (m-30) cc_final: 0.7971 (m-30) REVERT: A 465 ASN cc_start: 0.9326 (t0) cc_final: 0.9016 (t0) outliers start: 5 outliers final: 4 residues processed: 38 average time/residue: 0.1181 time to fit residues: 6.0807 Evaluate side-chains 37 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 33 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.0470 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 11 optimal weight: 0.0570 chunk 32 optimal weight: 0.0470 chunk 23 optimal weight: 0.7980 overall best weight: 0.3494 ------------------------------------------------------------------------------- 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: 0.8136 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3454 Z= 0.140 Angle : 0.530 8.153 4677 Z= 0.260 Chirality : 0.040 0.241 535 Planarity : 0.004 0.063 555 Dihedral : 11.048 88.339 533 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.56 % Allowed : 15.41 % Favored : 84.03 % 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: 2.18 (0.46), residues: 396 helix: 3.72 (0.37), residues: 206 sheet: 0.83 (0.66), residues: 63 loop : -2.42 (0.50), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 439 HIS 0.002 0.001 HIS A 171 PHE 0.009 0.001 PHE A 55 TYR 0.011 0.001 TYR A 340 ARG 0.002 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.393 Fit side-chains REVERT: A 141 PHE cc_start: 0.7908 (m-80) cc_final: 0.7601 (m-80) REVERT: A 442 ASP cc_start: 0.8347 (m-30) cc_final: 0.8030 (m-30) REVERT: A 465 ASN cc_start: 0.9312 (t0) cc_final: 0.9004 (t0) outliers start: 2 outliers final: 2 residues processed: 41 average time/residue: 0.1232 time to fit residues: 6.8903 Evaluate side-chains 39 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 357 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 0.0670 chunk 26 optimal weight: 0.1980 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 0.0870 chunk 31 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 25 optimal weight: 0.3980 overall best weight: 0.2696 ------------------------------------------------------------------------------- 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: 0.8105 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3454 Z= 0.135 Angle : 0.520 8.103 4677 Z= 0.255 Chirality : 0.038 0.230 535 Planarity : 0.004 0.062 555 Dihedral : 10.767 91.982 533 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.84 % Allowed : 15.69 % Favored : 83.47 % 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: 2.16 (0.46), residues: 396 helix: 3.74 (0.36), residues: 206 sheet: 0.72 (0.65), residues: 63 loop : -2.44 (0.50), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 82 HIS 0.001 0.000 HIS A 171 PHE 0.008 0.001 PHE A 60 TYR 0.009 0.001 TYR A 340 ARG 0.002 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.404 Fit side-chains REVERT: A 141 PHE cc_start: 0.7933 (m-80) cc_final: 0.7686 (m-80) REVERT: A 441 ASP cc_start: 0.8258 (p0) cc_final: 0.7813 (p0) REVERT: A 442 ASP cc_start: 0.8318 (m-30) cc_final: 0.7947 (m-30) REVERT: A 465 ASN cc_start: 0.9309 (t0) cc_final: 0.9025 (t0) outliers start: 3 outliers final: 2 residues processed: 43 average time/residue: 0.1344 time to fit residues: 7.8639 Evaluate side-chains 41 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 357 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.5980 chunk 9 optimal weight: 0.0870 chunk 29 optimal weight: 0.0170 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 0.0770 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.3154 ------------------------------------------------------------------------------- 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: 0.8102 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3454 Z= 0.134 Angle : 0.524 8.098 4677 Z= 0.256 Chirality : 0.038 0.206 535 Planarity : 0.004 0.061 555 Dihedral : 10.597 93.350 533 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.56 % Allowed : 16.53 % Favored : 82.91 % 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: 2.16 (0.46), residues: 396 helix: 3.74 (0.36), residues: 206 sheet: 0.79 (0.65), residues: 63 loop : -2.46 (0.50), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 82 HIS 0.001 0.000 HIS A 187 PHE 0.008 0.001 PHE A 55 TYR 0.016 0.001 TYR A 83 ARG 0.002 0.000 ARG A 112 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.396 Fit side-chains REVERT: A 141 PHE cc_start: 0.7959 (m-80) cc_final: 0.7734 (m-80) REVERT: A 308 MET cc_start: 0.8810 (tpt) cc_final: 0.8398 (tpt) REVERT: A 441 ASP cc_start: 0.8280 (p0) cc_final: 0.7856 (p0) REVERT: A 442 ASP cc_start: 0.8351 (m-30) cc_final: 0.7978 (m-30) REVERT: A 465 ASN cc_start: 0.9319 (t0) cc_final: 0.9033 (t0) outliers start: 2 outliers final: 2 residues processed: 40 average time/residue: 0.1227 time to fit residues: 6.7238 Evaluate side-chains 40 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 357 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 0.0770 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 15 optimal weight: 0.0670 chunk 14 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.115680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.088145 restraints weight = 5514.558| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.24 r_work: 0.3056 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3454 Z= 0.147 Angle : 0.522 7.960 4677 Z= 0.255 Chirality : 0.038 0.203 535 Planarity : 0.004 0.061 555 Dihedral : 10.579 94.236 533 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.84 % Allowed : 16.53 % Favored : 82.63 % 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: 2.14 (0.46), residues: 396 helix: 3.72 (0.36), residues: 206 sheet: 0.76 (0.65), residues: 63 loop : -2.47 (0.50), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 82 HIS 0.001 0.000 HIS A 187 PHE 0.010 0.001 PHE A 55 TYR 0.013 0.001 TYR A 83 ARG 0.002 0.000 ARG A 112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1076.65 seconds wall clock time: 19 minutes 58.90 seconds (1198.90 seconds total)