Starting phenix.real_space_refine on Sun Mar 10 22:37:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b19_7031/03_2024/6b19_7031.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b19_7031/03_2024/6b19_7031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b19_7031/03_2024/6b19_7031.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b19_7031/03_2024/6b19_7031.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b19_7031/03_2024/6b19_7031.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b19_7031/03_2024/6b19_7031.pdb" } resolution = 4.5 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= 0.006 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 37 5.49 5 C 3032 2.51 5 N 1054 2.21 5 O 1167 1.98 5 H 409 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5699 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 2512 Classifications: {'peptide': 508} Incomplete info: {'truncation_to_alanine': 456} Link IDs: {'CIS': 1, 'PTRANS': 33, 'TRANS': 473} Chain breaks: 11 Unresolved chain link angles: 33 Unresolved non-hydrogen bonds: 1751 Unresolved non-hydrogen angles: 2259 Unresolved non-hydrogen dihedrals: 1501 Unresolved non-hydrogen chiralities: 154 Planarities with less than four sites: {'GLN:plan1': 34, 'HIS:plan': 8, 'TYR:plan': 22, 'ASN:plan1': 18, 'TRP:plan': 17, 'ASP:plan': 21, 'PHE:plan': 12, 'GLU:plan': 42, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 915 Chain: "B" Number of atoms: 1974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 1974 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 363} Link IDs: {'PTRANS': 28, 'TRANS': 370} Chain breaks: 7 Unresolved chain link angles: 28 Unresolved non-hydrogen bonds: 1417 Unresolved non-hydrogen angles: 1829 Unresolved non-hydrogen dihedrals: 1227 Unresolved non-hydrogen chiralities: 120 Planarities with less than four sites: {'GLN:plan1': 24, 'HIS:plan': 6, 'TYR:plan': 16, 'ASN:plan1': 12, 'TRP:plan': 16, 'ASP:plan': 18, 'PHE:plan': 11, 'GLU:plan': 35, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 743 Chain: "C" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 612 Classifications: {'RNA': 19} Modifications used: {'5*END': 1, 'rna3p_pur': 11, 'rna3p_pyr': 7} Link IDs: {'rna3p': 18} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 601 Classifications: {'DNA': 2, 'RNA': 17} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 11} Link IDs: {'rna3p': 18} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.22, per 1000 atoms: 0.74 Number of scatterers: 5699 At special positions: 0 Unit cell: (96, 110, 91, 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) P 37 15.00 O 1167 8.00 N 1054 7.00 C 3032 6.00 H 409 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 3.73 Conformation dependent library (CDL) restraints added in 1.2 seconds 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1716 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 8 sheets defined 37.3% alpha, 5.4% beta 19 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 33 through 44 removed outlier: 4.276A pdb=" N THR A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 83 Processing helix chain 'A' and resid 155 through 175 removed outlier: 3.617A pdb=" N ILE A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 196 through 211 removed outlier: 3.633A pdb=" N LYS A 201 " --> pdb=" O GLN A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 276 through 283 removed outlier: 4.006A pdb=" N LEU A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 312 removed outlier: 3.520A pdb=" N LEU A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 383 Processing helix chain 'A' and resid 394 through 403 Processing helix chain 'A' and resid 473 through 489 removed outlier: 3.699A pdb=" N ASP A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 508 removed outlier: 3.946A pdb=" N LEU A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 528 Processing helix chain 'A' and resid 545 through 550 Processing helix chain 'B' and resid 28 through 45 removed outlier: 3.680A pdb=" N VAL B 35 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N GLU B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 84 Processing helix chain 'B' and resid 84 through 92 removed outlier: 4.035A pdb=" N TRP B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 122 through 126 removed outlier: 4.003A pdb=" N LYS B 126 " --> pdb=" O ASP B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 154 through 160 Processing helix chain 'B' and resid 160 through 175 Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 194 through 212 Processing helix chain 'B' and resid 253 through 268 Processing helix chain 'B' and resid 278 through 283 Processing helix chain 'B' and resid 296 through 312 Processing helix chain 'B' and resid 363 through 384 Processing helix chain 'B' and resid 394 through 402 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AA2, first strand: chain 'A' and resid 179 through 180 removed outlier: 3.545A pdb=" N VAL A 179 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 350 through 353 removed outlier: 4.936A pdb=" N GLN A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 328 " --> pdb=" O GLN A 340 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE A 329 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE A 389 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 441 through 443 Processing sheet with id=AA5, first strand: chain 'A' and resid 492 through 493 Processing sheet with id=AA6, first strand: chain 'B' and resid 61 through 63 Processing sheet with id=AA7, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AA8, first strand: chain 'B' and resid 327 through 330 removed outlier: 6.634A pdb=" N ILE B 341 " --> pdb=" O LEU B 349 " (cutoff:3.500A) 246 hydrogen bonds defined for protein. 690 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 3.02 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.75 - 1.20: 409 1.20 - 1.64: 5362 1.64 - 2.09: 0 2.09 - 2.53: 0 2.53 - 2.98: 1 Bond restraints: 5772 Sorted by residual: bond pdb=" C THR A 286 " pdb=" N LEU A 289 " ideal model delta sigma weight residual 1.329 2.978 -1.649 1.40e-02 5.10e+03 1.39e+04 bond pdb=" N6 A C 191 " pdb=" H61 A C 191 " ideal model delta sigma weight residual 0.860 0.751 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" N6 A C 191 " pdb=" H62 A C 191 " ideal model delta sigma weight residual 0.860 0.925 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" C1' A C 191 " pdb=" N9 A C 191 " ideal model delta sigma weight residual 1.475 1.445 0.030 1.50e-02 4.44e+03 3.93e+00 bond pdb=" C ILE B 178 " pdb=" N VAL B 179 " ideal model delta sigma weight residual 1.328 1.282 0.046 2.53e-02 1.56e+03 3.24e+00 ... (remaining 5767 not shown) Histogram of bond angle deviations from ideal: 41.19 - 63.53: 1 63.53 - 85.87: 0 85.87 - 108.21: 582 108.21 - 130.55: 7926 130.55 - 152.89: 12 Bond angle restraints: 8521 Sorted by residual: angle pdb=" O THR A 286 " pdb=" C THR A 286 " pdb=" N LEU A 289 " ideal model delta sigma weight residual 122.59 41.19 81.40 1.33e+00 5.65e-01 3.75e+03 angle pdb=" CA THR A 286 " pdb=" C THR A 286 " pdb=" N LEU A 289 " ideal model delta sigma weight residual 116.84 152.89 -36.05 1.71e+00 3.42e-01 4.45e+02 angle pdb=" C ASN A 54 " pdb=" N PRO A 55 " pdb=" CA PRO A 55 " ideal model delta sigma weight residual 119.84 128.00 -8.16 1.25e+00 6.40e-01 4.26e+01 angle pdb=" C THR A 397 " pdb=" N TRP A 398 " pdb=" CA TRP A 398 " ideal model delta sigma weight residual 120.29 114.26 6.03 1.42e+00 4.96e-01 1.80e+01 angle pdb=" C THR A 286 " pdb=" N LEU A 289 " pdb=" CA LEU A 289 " ideal model delta sigma weight residual 121.70 114.45 7.25 1.80e+00 3.09e-01 1.62e+01 ... (remaining 8516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.31: 3152 29.31 - 58.62: 71 58.62 - 87.93: 53 87.93 - 117.24: 2 117.24 - 146.55: 2 Dihedral angle restraints: 3280 sinusoidal: 677 harmonic: 2603 Sorted by residual: dihedral pdb=" CA GLU A 413 " pdb=" C GLU A 413 " pdb=" N TRP A 414 " pdb=" CA TRP A 414 " ideal model delta harmonic sigma weight residual -180.00 -160.37 -19.63 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA ASN B 418 " pdb=" C ASN B 418 " pdb=" N THR B 419 " pdb=" CA THR B 419 " ideal model delta harmonic sigma weight residual -180.00 -160.86 -19.14 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA THR A 286 " pdb=" C THR A 286 " pdb=" N LEU A 289 " pdb=" CA LEU A 289 " ideal model delta harmonic sigma weight residual 0.00 18.13 -18.13 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 3277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 665 0.039 - 0.078: 250 0.078 - 0.118: 106 0.118 - 0.157: 19 0.157 - 0.196: 3 Chirality restraints: 1043 Sorted by residual: chirality pdb=" C3' G C 181 " pdb=" C4' G C 181 " pdb=" O3' G C 181 " pdb=" C2' G C 181 " both_signs ideal model delta sigma weight residual False -2.50 -2.30 -0.20 2.00e-01 2.50e+01 9.59e-01 chirality pdb=" CA THR B 240 " pdb=" N THR B 240 " pdb=" C THR B 240 " pdb=" CB THR B 240 " both_signs ideal model delta sigma weight residual False 2.53 2.70 -0.18 2.00e-01 2.50e+01 7.74e-01 chirality pdb=" CA LEU B 368 " pdb=" N LEU B 368 " pdb=" C LEU B 368 " pdb=" CB LEU B 368 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.56e-01 ... (remaining 1040 not shown) Planarity restraints: 958 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 286 " -0.201 2.00e-02 2.50e+03 1.73e-01 2.99e+02 pdb=" C THR A 286 " 0.240 2.00e-02 2.50e+03 pdb=" O THR A 286 " 0.082 2.00e-02 2.50e+03 pdb=" N LEU A 289 " -0.122 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 41 " 0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C MET A 41 " -0.062 2.00e-02 2.50e+03 pdb=" O MET A 41 " 0.023 2.00e-02 2.50e+03 pdb=" N GLU A 42 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 296 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C THR B 296 " 0.059 2.00e-02 2.50e+03 pdb=" O THR B 296 " -0.022 2.00e-02 2.50e+03 pdb=" N GLU B 297 " -0.020 2.00e-02 2.50e+03 ... (remaining 955 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.34: 282 2.34 - 2.91: 4305 2.91 - 3.47: 8362 3.47 - 4.04: 11082 4.04 - 4.60: 14332 Nonbonded interactions: 38363 Sorted by model distance: nonbonded pdb=" H2' G D 69 " pdb=" H8 G D 70 " model vdw 1.781 2.270 nonbonded pdb=" H2' C D 72 " pdb=" H8 G D 73 " model vdw 1.806 2.270 nonbonded pdb=" H2' G C 186 " pdb=" H6 C C 187 " model vdw 1.839 2.270 nonbonded pdb=" H2' G D 73 " pdb=" H6 C D 74 " model vdw 1.853 2.270 nonbonded pdb=" H2' G C 183 " pdb=" H8 G C 184 " model vdw 1.863 2.270 ... (remaining 38358 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: 0.620 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: 0.170 Extract box with map and model: 2.700 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 25.190 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6326 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 : 0.023 1.649 5363 Z= 1.967 Angle : 1.382 81.401 7585 Z= 0.937 Chirality : 0.048 0.196 1043 Planarity : 0.008 0.173 925 Dihedral : 15.602 74.879 1477 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 19.42 % Favored : 80.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -5.73 (0.22), residues: 865 helix: -2.49 (0.24), residues: 298 sheet: -3.46 (0.48), residues: 95 loop : -5.02 (0.21), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 24 PHE 0.000 0.000 PHE A 61 TYR 0.000 0.000 TYR A 56 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.596 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0619 time to fit residues: 1.8937 Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 38 optimal weight: 30.0000 chunk 23 optimal weight: 0.0040 chunk 46 optimal weight: 30.0000 chunk 36 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 40.0000 chunk 53 optimal weight: 30.0000 chunk 82 optimal weight: 40.0000 overall best weight: 5.6000 ------------------------------------------------------------------------------- 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: 0.6492 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5363 Z= 0.211 Angle : 0.631 6.150 7585 Z= 0.355 Chirality : 0.042 0.179 1043 Planarity : 0.003 0.025 925 Dihedral : 15.645 74.533 1477 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.45 % Favored : 81.55 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -4.24 (0.26), residues: 867 helix: -0.43 (0.29), residues: 314 sheet: -3.63 (0.52), residues: 80 loop : -4.64 (0.21), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 24 PHE 0.000 0.000 PHE A 61 TYR 0.000 0.000 TYR A 56 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.598 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0551 time to fit residues: 1.8693 Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 30.0000 chunk 25 optimal weight: 50.0000 chunk 68 optimal weight: 4.9990 chunk 56 optimal weight: 50.0000 chunk 22 optimal weight: 9.9990 chunk 82 optimal weight: 0.3980 chunk 89 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 28 optimal weight: 50.0000 chunk 66 optimal weight: 0.2980 chunk 81 optimal weight: 50.0000 overall best weight: 4.7386 ------------------------------------------------------------------------------- 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: 0.6544 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 5363 Z= 0.176 Angle : 0.575 7.122 7585 Z= 0.317 Chirality : 0.041 0.141 1043 Planarity : 0.003 0.015 925 Dihedral : 15.514 74.111 1477 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.61 % Favored : 83.39 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -3.40 (0.27), residues: 867 helix: 0.53 (0.30), residues: 322 sheet: -2.81 (0.54), residues: 75 loop : -4.50 (0.23), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 24 PHE 0.000 0.000 PHE A 61 TYR 0.000 0.000 TYR A 56 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.568 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0537 time to fit residues: 1.8228 Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 30.0000 chunk 42 optimal weight: 50.0000 chunk 9 optimal weight: 50.0000 chunk 39 optimal weight: 3.9990 chunk 55 optimal weight: 30.0000 chunk 83 optimal weight: 30.0000 chunk 87 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 78 optimal weight: 30.0000 chunk 23 optimal weight: 50.0000 chunk 73 optimal weight: 6.9990 overall best weight: 14.1996 ------------------------------------------------------------------------------- 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: 0.6738 moved from start: 0.5439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 5363 Z= 0.427 Angle : 1.006 9.559 7585 Z= 0.568 Chirality : 0.052 0.265 1043 Planarity : 0.005 0.021 925 Dihedral : 17.441 78.742 1477 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 48.81 Ramachandran Plot: Outliers : 0.46 % Allowed : 27.91 % Favored : 71.63 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -5.05 (0.24), residues: 867 helix: -1.49 (0.26), residues: 300 sheet: -2.92 (0.62), residues: 52 loop : -4.91 (0.21), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 24 PHE 0.000 0.000 PHE A 61 TYR 0.000 0.000 TYR A 56 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.598 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0565 time to fit residues: 1.9110 Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 50.0000 chunk 1 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 44 optimal weight: 30.0000 chunk 78 optimal weight: 10.0000 chunk 22 optimal weight: 40.0000 chunk 29 optimal weight: 40.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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: 0.6689 moved from start: 0.5565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5363 Z= 0.248 Angle : 0.726 8.889 7585 Z= 0.405 Chirality : 0.045 0.189 1043 Planarity : 0.003 0.014 925 Dihedral : 16.973 81.381 1477 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 32.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.91 % Favored : 75.09 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -4.66 (0.25), residues: 867 helix: -1.03 (0.28), residues: 311 sheet: -3.28 (0.60), residues: 58 loop : -4.77 (0.22), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 24 PHE 0.000 0.000 PHE A 61 TYR 0.000 0.000 TYR A 56 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.530 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0550 time to fit residues: 1.7882 Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 51 optimal weight: 40.0000 chunk 21 optimal weight: 20.0000 chunk 88 optimal weight: 40.0000 chunk 73 optimal weight: 6.9990 chunk 40 optimal weight: 50.0000 chunk 7 optimal weight: 50.0000 chunk 29 optimal weight: 30.0000 chunk 46 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 overall best weight: 9.5992 ------------------------------------------------------------------------------- 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: 0.6743 moved from start: 0.6475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5363 Z= 0.296 Angle : 0.817 9.562 7585 Z= 0.456 Chirality : 0.047 0.226 1043 Planarity : 0.004 0.017 925 Dihedral : 17.779 93.233 1477 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 38.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 30.45 % Favored : 69.55 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -4.86 (0.25), residues: 867 helix: -1.10 (0.29), residues: 294 sheet: -3.44 (0.58), residues: 58 loop : -4.84 (0.22), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 24 PHE 0.000 0.000 PHE A 61 TYR 0.000 0.000 TYR A 56 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.575 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0502 time to fit residues: 1.7306 Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 50.0000 chunk 50 optimal weight: 30.0000 chunk 64 optimal weight: 3.9990 chunk 49 optimal weight: 40.0000 chunk 74 optimal weight: 20.0000 chunk 87 optimal weight: 0.7980 chunk 54 optimal weight: 30.0000 chunk 53 optimal weight: 30.0000 chunk 40 optimal weight: 50.0000 chunk 35 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 overall best weight: 8.5592 ------------------------------------------------------------------------------- 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: 0.6723 moved from start: 0.6737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5363 Z= 0.256 Angle : 0.741 9.039 7585 Z= 0.412 Chirality : 0.045 0.188 1043 Planarity : 0.003 0.014 925 Dihedral : 17.735 96.819 1477 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 34.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 27.10 % Favored : 72.90 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -4.78 (0.25), residues: 867 helix: -1.06 (0.29), residues: 303 sheet: -3.54 (0.57), residues: 60 loop : -4.81 (0.22), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 24 PHE 0.000 0.000 PHE A 61 TYR 0.000 0.000 TYR A 56 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.546 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0531 time to fit residues: 1.8189 Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 50.0000 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 55 optimal weight: 30.0000 chunk 59 optimal weight: 50.0000 chunk 43 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 79 optimal weight: 30.0000 chunk 84 optimal weight: 5.9990 chunk 76 optimal weight: 30.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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: 0.6663 moved from start: 0.6699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 5363 Z= 0.158 Angle : 0.580 6.639 7585 Z= 0.320 Chirality : 0.042 0.142 1043 Planarity : 0.002 0.011 925 Dihedral : 17.247 93.858 1477 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 24.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.07 % Favored : 76.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -4.13 (0.27), residues: 867 helix: -0.24 (0.30), residues: 313 sheet: -3.80 (0.49), residues: 81 loop : -4.59 (0.23), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 24 PHE 0.000 0.000 PHE A 61 TYR 0.000 0.000 TYR A 56 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.598 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0575 time to fit residues: 1.9380 Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 50.0000 chunk 84 optimal weight: 10.0000 chunk 49 optimal weight: 40.0000 chunk 35 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 25 optimal weight: 30.0000 chunk 73 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 53 optimal weight: 40.0000 chunk 86 optimal weight: 50.0000 chunk 52 optimal weight: 4.9990 overall best weight: 8.1992 ------------------------------------------------------------------------------- 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: 0.6730 moved from start: 0.7095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5363 Z= 0.257 Angle : 0.732 8.167 7585 Z= 0.410 Chirality : 0.045 0.207 1043 Planarity : 0.003 0.015 925 Dihedral : 17.857 100.459 1477 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 35.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 29.53 % Favored : 70.47 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -4.45 (0.26), residues: 867 helix: -0.59 (0.30), residues: 305 sheet: -3.68 (0.56), residues: 62 loop : -4.73 (0.22), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 24 PHE 0.000 0.000 PHE A 61 TYR 0.000 0.000 TYR A 56 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.598 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0558 time to fit residues: 1.8882 Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 30.0000 chunk 60 optimal weight: 6.9990 chunk 90 optimal weight: 20.0000 chunk 83 optimal weight: 30.0000 chunk 72 optimal weight: 40.0000 chunk 7 optimal weight: 50.0000 chunk 55 optimal weight: 30.0000 chunk 44 optimal weight: 30.0000 chunk 57 optimal weight: 50.0000 chunk 76 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 overall best weight: 15.1994 ------------------------------------------------------------------------------- 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: 0.6817 moved from start: 0.7915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 5363 Z= 0.432 Angle : 1.018 9.948 7585 Z= 0.571 Chirality : 0.051 0.256 1043 Planarity : 0.005 0.022 925 Dihedral : 18.806 105.803 1477 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 56.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 35.41 % Favored : 64.59 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -5.59 (0.23), residues: 867 helix: -1.86 (0.27), residues: 282 sheet: -4.29 (0.56), residues: 52 loop : -5.08 (0.20), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 24 PHE 0.000 0.000 PHE A 61 TYR 0.000 0.000 TYR A 56 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.566 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0562 time to fit residues: 1.8682 Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 72 optimal weight: 40.0000 chunk 30 optimal weight: 9.9990 chunk 74 optimal weight: 20.0000 chunk 9 optimal weight: 0.0370 chunk 13 optimal weight: 0.3980 chunk 63 optimal weight: 50.0000 chunk 4 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 overall best weight: 5.8866 ------------------------------------------------------------------------------- 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 = 0.3701 r_free = 0.3701 target = 0.075341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.061699 restraints weight = 64133.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.061816 restraints weight = 56488.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.061591 restraints weight = 53173.162| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.7642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5363 Z= 0.197 Angle : 0.660 6.929 7585 Z= 0.368 Chirality : 0.044 0.172 1043 Planarity : 0.003 0.013 925 Dihedral : 17.803 97.462 1477 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 30.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.22 % Favored : 75.78 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -4.85 (0.25), residues: 867 helix: -1.03 (0.28), residues: 305 sheet: -3.85 (0.48), residues: 76 loop : -4.89 (0.21), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 24 PHE 0.000 0.000 PHE A 61 TYR 0.000 0.000 TYR A 56 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1151.96 seconds wall clock time: 21 minutes 23.50 seconds (1283.50 seconds total)