Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 4 00:18:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b19_7031/07_2023/6b19_7031.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b19_7031/07_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_7031/07_2023/6b19_7031.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b19_7031/07_2023/6b19_7031.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b19_7031/07_2023/6b19_7031.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b19_7031/07_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 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-1.21rc1-5013/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: 3.92, per 1000 atoms: 0.69 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: 3.46 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: 1.72 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: 2.01 Time building geometry restraints manager: 3.60 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: 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 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: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.200 Extract box with map and model: 2.900 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 22.870 Find NCS groups from input model: 0.160 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: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.800 ------------------------------------------------------------------------------- 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 : 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 : 0.510 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0641 time to fit residues: 1.8969 Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.522 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6990 ------------------------------------------------------------------------------- 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: 0.6481 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 5363 Z= 0.209 Angle : 0.635 6.673 7585 Z= 0.357 Chirality : 0.042 0.177 1043 Planarity : 0.003 0.017 925 Dihedral : 7.373 66.810 1329 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.69 % Favored : 81.31 % 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: -4.26 (0.26), residues: 867 helix: -0.50 (0.29), residues: 316 sheet: -3.66 (0.52), residues: 80 loop : -4.63 (0.21), residues: 471 *********************** 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 : 0.564 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0552 time to fit residues: 1.8437 Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.562 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6856 ------------------------------------------------------------------------------- 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: 5.9990 chunk 56 optimal weight: 50.0000 chunk 22 optimal weight: 30.0000 chunk 82 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 28 optimal weight: 50.0000 chunk 66 optimal weight: 0.8980 chunk 81 optimal weight: 50.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- 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: 0.6538 moved from start: 0.3374 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= 0.174 Angle : 0.564 6.082 7585 Z= 0.313 Chirality : 0.041 0.145 1043 Planarity : 0.002 0.015 925 Dihedral : 7.497 68.744 1329 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.96 % Favored : 83.04 % 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: -3.43 (0.27), residues: 867 helix: 0.52 (0.30), residues: 323 sheet: -2.87 (0.54), residues: 75 loop : -4.53 (0.22), residues: 469 *********************** 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 : 0.686 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0660 time to fit residues: 2.2421 Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.680 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7409 ------------------------------------------------------------------------------- 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: 20.0000 chunk 42 optimal weight: 50.0000 chunk 9 optimal weight: 50.0000 chunk 39 optimal weight: 30.0000 chunk 55 optimal weight: 30.0000 chunk 83 optimal weight: 30.0000 chunk 87 optimal weight: 20.0000 chunk 43 optimal weight: 30.0000 chunk 78 optimal weight: 30.0000 chunk 23 optimal weight: 50.0000 chunk 73 optimal weight: 7.9990 overall best weight: 21.5998 ------------------------------------------------------------------------------- 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: 0.6079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.055 5363 Z= 0.579 Angle : 1.294 10.483 7585 Z= 0.728 Chirality : 0.058 0.310 1043 Planarity : 0.007 0.024 925 Dihedral : 13.166 83.008 1329 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 75.12 Ramachandran Plot: Outliers : 2.19 % Allowed : 31.26 % Favored : 66.55 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: -6.22 (0.22), residues: 867 helix: -2.89 (0.23), residues: 287 sheet: -4.23 (0.49), residues: 64 loop : -5.19 (0.21), residues: 516 *********************** 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 : 0.586 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0564 time to fit residues: 1.8990 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: 0.7077 ------------------------------------------------------------------------------- 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: 30.0000 chunk 1 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 44 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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: 0.6703 moved from start: 0.5721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 5363 Z= 0.240 Angle : 0.737 8.597 7585 Z= 0.413 Chirality : 0.045 0.200 1043 Planarity : 0.003 0.015 925 Dihedral : 11.452 83.045 1329 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 32.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.91 % Favored : 75.09 % 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: -5.27 (0.24), residues: 867 helix: -1.85 (0.26), residues: 310 sheet: -3.65 (0.58), residues: 58 loop : -4.88 (0.22), residues: 499 *********************** 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 : 0.571 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0551 time to fit residues: 1.8539 Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.580 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6587 ------------------------------------------------------------------------------- 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: 50.0000 chunk 17 optimal weight: 30.0000 chunk 51 optimal weight: 30.0000 chunk 21 optimal weight: 10.0000 chunk 88 optimal weight: 40.0000 chunk 73 optimal weight: 5.9990 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: 20.0000 overall best weight: 17.1998 ------------------------------------------------------------------------------- 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: 0.6828 moved from start: 0.7256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.044 5363 Z= 0.474 Angle : 1.140 11.104 7585 Z= 0.635 Chirality : 0.054 0.263 1043 Planarity : 0.006 0.023 925 Dihedral : 14.214 107.492 1329 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 68.02 Ramachandran Plot: Outliers : 0.92 % Allowed : 38.06 % Favored : 61.01 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -6.09 (0.23), residues: 867 helix: -2.81 (0.25), residues: 277 sheet: -4.32 (0.55), residues: 60 loop : -5.04 (0.21), residues: 530 *********************** 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 : 0.499 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0523 time to fit residues: 1.7037 Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.552 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6563 ------------------------------------------------------------------------------- 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: 5.9990 chunk 49 optimal weight: 0.0970 chunk 74 optimal weight: 20.0000 chunk 87 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 40 optimal weight: 50.0000 chunk 35 optimal weight: 20.0000 chunk 52 optimal weight: 7.9990 overall best weight: 6.2188 ------------------------------------------------------------------------------- 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: 0.6715 moved from start: 0.6814 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= 0.204 Angle : 0.685 8.248 7585 Z= 0.382 Chirality : 0.044 0.172 1043 Planarity : 0.003 0.017 925 Dihedral : 12.492 95.090 1329 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 30.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.88 % Favored : 76.12 % 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: -5.28 (0.24), residues: 867 helix: -1.76 (0.27), residues: 300 sheet: -3.93 (0.50), residues: 72 loop : -4.87 (0.22), residues: 495 *********************** 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 : 0.502 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0581 time to fit residues: 1.8862 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7130 ------------------------------------------------------------------------------- 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: 10.0000 chunk 17 optimal weight: 40.0000 chunk 16 optimal weight: 5.9990 chunk 55 optimal weight: 30.0000 chunk 59 optimal weight: 50.0000 chunk 43 optimal weight: 6.9990 chunk 8 optimal weight: 30.0000 chunk 68 optimal weight: 20.0000 chunk 79 optimal weight: 0.0770 chunk 84 optimal weight: 20.0000 chunk 76 optimal weight: 30.0000 overall best weight: 8.6150 ------------------------------------------------------------------------------- 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: 0.6751 moved from start: 0.7150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 5363 Z= 0.263 Angle : 0.762 8.870 7585 Z= 0.426 Chirality : 0.046 0.200 1043 Planarity : 0.003 0.016 925 Dihedral : 12.930 102.044 1329 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 37.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 33.91 % Favored : 66.09 % 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: -5.22 (0.25), residues: 867 helix: -1.54 (0.28), residues: 293 sheet: -3.92 (0.51), residues: 72 loop : -4.91 (0.22), residues: 502 *********************** 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 : 0.569 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0562 time to fit residues: 1.8700 Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.564 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6835 ------------------------------------------------------------------------------- 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: 20.0000 chunk 49 optimal weight: 50.0000 chunk 35 optimal weight: 20.0000 chunk 64 optimal weight: 0.6980 chunk 25 optimal weight: 20.0000 chunk 73 optimal weight: 5.9990 chunk 77 optimal weight: 20.0000 chunk 53 optimal weight: 40.0000 chunk 86 optimal weight: 50.0000 chunk 52 optimal weight: 9.9990 overall best weight: 11.3392 ------------------------------------------------------------------------------- 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: 0.6792 moved from start: 0.7750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.033 5363 Z= 0.337 Angle : 0.890 9.408 7585 Z= 0.499 Chirality : 0.048 0.241 1043 Planarity : 0.004 0.019 925 Dihedral : 13.757 104.890 1329 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 47.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 33.56 % Favored : 66.44 % 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: -5.46 (0.24), residues: 867 helix: -1.87 (0.27), residues: 279 sheet: -3.78 (0.67), residues: 48 loop : -4.95 (0.21), residues: 540 *********************** 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 : 0.631 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0582 time to fit residues: 1.9436 Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.599 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7311 ------------------------------------------------------------------------------- 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: 0.9980 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: 20.0000 chunk 44 optimal weight: 20.0000 chunk 57 optimal weight: 40.0000 chunk 76 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 overall best weight: 10.5992 ------------------------------------------------------------------------------- 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: 0.6781 moved from start: 0.7959 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= 0.308 Angle : 0.827 8.312 7585 Z= 0.464 Chirality : 0.047 0.208 1043 Planarity : 0.004 0.017 925 Dihedral : 13.568 103.211 1329 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 42.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 34.60 % 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 : 0.00 % 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: -5.46 (0.24), residues: 867 helix: -1.79 (0.28), residues: 279 sheet: -3.88 (0.64), residues: 50 loop : -4.98 (0.21), residues: 538 ********************** 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 : 0.593 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0557 time to fit residues: 1.8951 Evaluate side-chains 10 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.593 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6838 ------------------------------------------------------------------------------- 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: 0.0050 chunk 20 optimal weight: 0.0770 chunk 72 optimal weight: 40.0000 chunk 30 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 chunk 9 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 63 optimal weight: 50.0000 chunk 4 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 overall best weight: 5.6158 ------------------------------------------------------------------------------- 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 = 0.075418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.061954 restraints weight = 64182.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.062085 restraints weight = 55700.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.061872 restraints weight = 54248.445| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.7806 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= 0.195 Angle : 0.641 5.930 7585 Z= 0.358 Chirality : 0.043 0.159 1043 Planarity : 0.003 0.015 925 Dihedral : 12.732 99.320 1329 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 28.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.37 % Favored : 74.63 % 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: -4.85 (0.25), residues: 867 helix: -1.05 (0.29), residues: 299 sheet: -3.84 (0.57), residues: 66 loop : -4.84 (0.22), residues: 502 =============================================================================== Job complete usr+sys time: 1055.28 seconds wall clock time: 19 minutes 38.68 seconds (1178.68 seconds total)