Starting phenix.real_space_refine (version: dev) on Fri Feb 17 17:13:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b19_7031/02_2023/6b19_7031.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b19_7031/02_2023/6b19_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_7031/02_2023/6b19_7031.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b19_7031/02_2023/6b19_7031.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b19_7031/02_2023/6b19_7031.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b19_7031/02_2023/6b19_7031.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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-4877/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: 4.28, per 1000 atoms: 0.75 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: 3.39 Conformation dependent library (CDL) restraints added in 1.0 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: 1.74 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: 2.02 Time building geometry restraints manager: 3.49 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 GLN A 367 " pdb=" CA GLN A 367 " pdb=" CB GLN A 367 " ideal model delta sigma weight residual 110.79 104.58 6.21 1.66e+00 3.63e-01 1.40e+01 ... (remaining 8516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.31: 3087 29.31 - 58.62: 13 58.62 - 87.93: 10 87.93 - 117.24: 2 117.24 - 146.55: 2 Dihedral angle restraints: 3114 sinusoidal: 511 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 3111 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 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. 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: 0.440 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: 0.190 Extract box with map and model: 2.880 Check model and map are aligned: 0.080 Process input model: 22.620 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.060 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 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 : 1.383 81.401 7585 Z= 0.937 Chirality : 0.048 0.196 1043 Planarity : 0.008 0.173 925 Dihedral : 6.447 63.060 1329 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 % 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 *********************** 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 : 0.563 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0625 time to fit residues: 1.9720 Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.591 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7271 ------------------------------------------------------------------------------- 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: 0.6505 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 5363 Z= 0.206 Angle : 0.646 11.899 7585 Z= 0.360 Chirality : 0.043 0.178 1043 Planarity : 0.003 0.035 925 Dihedral : 7.542 67.264 1329 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.22 % Favored : 81.78 % Rotamer Outliers : 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: -4.27 (0.25), residues: 867 helix: -0.47 (0.29), residues: 314 sheet: -3.63 (0.52), residues: 80 loop : -4.64 (0.21), residues: 473 *********************** 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 : 0.578 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0566 time to fit residues: 1.9268 Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.605 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6553 ------------------------------------------------------------------------------- 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: 40.0000 chunk 25 optimal weight: 50.0000 chunk 68 optimal weight: 1.9990 chunk 56 optimal weight: 50.0000 chunk 22 optimal weight: 30.0000 chunk 82 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 73 optimal weight: 30.0000 chunk 28 optimal weight: 50.0000 chunk 66 optimal weight: 0.0370 chunk 81 optimal weight: 50.0000 overall best weight: 10.0068 ------------------------------------------------------------------------------- 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: 0.6687 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 5363 Z= 0.326 Angle : 0.861 10.775 7585 Z= 0.481 Chirality : 0.047 0.272 1043 Planarity : 0.004 0.018 925 Dihedral : 10.272 78.631 1329 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 37.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.11 % Favored : 75.89 % Rotamer Outliers : 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: -4.67 (0.25), residues: 867 helix: -1.09 (0.27), residues: 311 sheet: -2.73 (0.66), residues: 52 loop : -4.80 (0.22), residues: 504 *********************** 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 : 0.574 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0573 time to fit residues: 2.0053 Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.508 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6175 ------------------------------------------------------------------------------- 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: 9.9990 chunk 42 optimal weight: 50.0000 chunk 9 optimal weight: 50.0000 chunk 39 optimal weight: 30.0000 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 43 optimal weight: 30.0000 chunk 78 optimal weight: 40.0000 chunk 23 optimal weight: 50.0000 chunk 73 optimal weight: 20.0000 overall best weight: 6.7188 ------------------------------------------------------------------------------- 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: 0.6646 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 5363 Z= 0.211 Angle : 0.650 9.161 7585 Z= 0.361 Chirality : 0.043 0.161 1043 Planarity : 0.003 0.013 925 Dihedral : 9.573 74.785 1329 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 26.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.99 % Favored : 79.01 % Rotamer Outliers : 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: -4.10 (0.26), residues: 867 helix: -0.34 (0.29), residues: 317 sheet: -2.85 (0.57), residues: 67 loop : -4.69 (0.23), residues: 483 *********************** 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 : 0.588 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0586 time to fit residues: 1.9006 Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.591 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6920 ------------------------------------------------------------------------------- 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: 40.0000 chunk 1 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 75 optimal weight: 30.0000 chunk 60 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 44 optimal weight: 30.0000 chunk 78 optimal weight: 0.3980 chunk 22 optimal weight: 20.0000 chunk 29 optimal weight: 30.0000 overall best weight: 5.4790 ------------------------------------------------------------------------------- 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: 0.6641 moved from start: 0.5278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 5363 Z= 0.189 Angle : 0.613 8.793 7585 Z= 0.338 Chirality : 0.042 0.162 1043 Planarity : 0.002 0.015 925 Dihedral : 9.651 78.145 1329 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 26.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.91 % Favored : 78.09 % Rotamer Outliers : 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: -3.71 (0.27), residues: 867 helix: 0.23 (0.30), residues: 313 sheet: -3.12 (0.58), residues: 62 loop : -4.53 (0.23), residues: 492 *********************** 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 : 0.648 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0577 time to fit residues: 2.0497 Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.563 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7240 ------------------------------------------------------------------------------- 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: 30.0000 chunk 17 optimal weight: 30.0000 chunk 51 optimal weight: 40.0000 chunk 21 optimal weight: 20.0000 chunk 88 optimal weight: 50.0000 chunk 73 optimal weight: 6.9990 chunk 40 optimal weight: 50.0000 chunk 7 optimal weight: 50.0000 chunk 29 optimal weight: 40.0000 chunk 46 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 overall best weight: 17.3996 ------------------------------------------------------------------------------- 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: 0.6808 moved from start: 0.6928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.043 5363 Z= 0.472 Angle : 1.114 11.120 7585 Z= 0.623 Chirality : 0.054 0.279 1043 Planarity : 0.006 0.023 925 Dihedral : 13.707 102.558 1329 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 63.68 Ramachandran Plot: Outliers : 0.58 % Allowed : 34.03 % Favored : 65.40 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -5.64 (0.23), residues: 867 helix: -2.19 (0.26), residues: 282 sheet: -3.67 (0.58), residues: 54 loop : -4.99 (0.21), residues: 531 *********************** 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 : 0.584 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0563 time to fit residues: 1.9051 Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.584 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7072 ------------------------------------------------------------------------------- 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: 20.0000 chunk 50 optimal weight: 30.0000 chunk 64 optimal weight: 30.0000 chunk 49 optimal weight: 40.0000 chunk 74 optimal weight: 4.9990 chunk 87 optimal weight: 9.9990 chunk 54 optimal weight: 30.0000 chunk 53 optimal weight: 20.0000 chunk 40 optimal weight: 50.0000 chunk 35 optimal weight: 9.9990 chunk 52 optimal weight: 20.0000 overall best weight: 12.9994 ------------------------------------------------------------------------------- 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: 0.6785 moved from start: 0.7232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 5363 Z= 0.355 Angle : 0.913 10.556 7585 Z= 0.509 Chirality : 0.049 0.210 1043 Planarity : 0.005 0.017 925 Dihedral : 13.595 100.341 1329 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 48.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 32.76 % Favored : 67.24 % Rotamer Outliers : 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: -5.60 (0.23), residues: 867 helix: -2.10 (0.26), residues: 281 sheet: -4.06 (0.53), residues: 62 loop : -4.95 (0.22), residues: 524 *********************** 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 : 0.590 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0537 time to fit residues: 1.8366 Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.549 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6631 ------------------------------------------------------------------------------- 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: 6.9990 chunk 17 optimal weight: 30.0000 chunk 16 optimal weight: 5.9990 chunk 55 optimal weight: 20.0000 chunk 59 optimal weight: 50.0000 chunk 43 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 79 optimal weight: 30.0000 chunk 84 optimal weight: 6.9990 chunk 76 optimal weight: 0.1980 overall best weight: 5.0388 ------------------------------------------------------------------------------- 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: 0.6697 moved from start: 0.7027 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 : 0.624 7.324 7585 Z= 0.344 Chirality : 0.043 0.152 1043 Planarity : 0.002 0.014 925 Dihedral : 12.320 96.203 1329 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 27.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.84 % Favored : 77.16 % Rotamer Outliers : 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: -4.71 (0.25), residues: 867 helix: -1.11 (0.28), residues: 315 sheet: -3.69 (0.51), residues: 74 loop : -4.72 (0.23), residues: 478 *********************** 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 : 0.566 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0566 time to fit residues: 1.8666 Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.551 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6783 ------------------------------------------------------------------------------- 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: 9.9990 chunk 49 optimal weight: 50.0000 chunk 35 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 chunk 25 optimal weight: 40.0000 chunk 73 optimal weight: 20.0000 chunk 77 optimal weight: 9.9990 chunk 53 optimal weight: 40.0000 chunk 86 optimal weight: 30.0000 chunk 52 optimal weight: 6.9990 overall best weight: 10.7992 ------------------------------------------------------------------------------- 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: 0.6772 moved from start: 0.7483 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= 0.305 Angle : 0.822 9.075 7585 Z= 0.458 Chirality : 0.047 0.220 1043 Planarity : 0.004 0.017 925 Dihedral : 13.383 103.017 1329 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 41.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 33.79 % Favored : 66.21 % Rotamer Outliers : 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: -5.12 (0.25), residues: 867 helix: -1.23 (0.29), residues: 281 sheet: -3.98 (0.54), residues: 62 loop : -4.91 (0.21), residues: 524 *********************** 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 : 0.587 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0546 time to fit residues: 1.8030 Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.509 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6194 ------------------------------------------------------------------------------- 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: 40.0000 chunk 60 optimal weight: 9.9990 chunk 90 optimal weight: 20.0000 chunk 83 optimal weight: 20.0000 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: 40.0000 chunk 76 optimal weight: 0.3980 chunk 22 optimal weight: 7.9990 overall best weight: 11.6792 ------------------------------------------------------------------------------- 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: 0.6796 moved from start: 0.8018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.032 5363 Z= 0.334 Angle : 0.880 9.074 7585 Z= 0.493 Chirality : 0.048 0.230 1043 Planarity : 0.004 0.018 925 Dihedral : 13.866 103.604 1329 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 46.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 32.53 % Favored : 67.47 % Rotamer Outliers : 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: -5.44 (0.24), residues: 867 helix: -1.71 (0.29), residues: 276 sheet: -4.14 (0.53), residues: 60 loop : -4.96 (0.21), residues: 531 ********************** 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 : 0.624 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0567 time to fit residues: 1.9175 Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.588 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7161 ------------------------------------------------------------------------------- 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: 0.9980 chunk 20 optimal weight: 0.0970 chunk 72 optimal weight: 40.0000 chunk 30 optimal weight: 8.9990 chunk 74 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 chunk 63 optimal weight: 50.0000 chunk 4 optimal weight: 9.9990 chunk 52 optimal weight: 20.0000 overall best weight: 5.4184 ------------------------------------------------------------------------------- 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 = 0.3705 r_free = 0.3705 target = 0.075462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.061917 restraints weight = 63803.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.061899 restraints weight = 57582.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.061999 restraints weight = 52062.401| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.7825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 5363 Z= 0.192 Angle : 0.640 7.540 7585 Z= 0.355 Chirality : 0.043 0.161 1043 Planarity : 0.003 0.014 925 Dihedral : 12.788 98.032 1329 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 28.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.72 % Favored : 74.28 % Rotamer Outliers : 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: -4.89 (0.25), residues: 867 helix: -0.90 (0.29), residues: 296 sheet: -3.91 (0.54), residues: 66 loop : -4.97 (0.21), residues: 505 =============================================================================== Job complete usr+sys time: 1069.02 seconds wall clock time: 20 minutes 9.37 seconds (1209.37 seconds total)