Starting phenix.real_space_refine (version: dev) on Thu Feb 16 22:29:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8di5_27439/02_2023/8di5_27439.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8di5_27439/02_2023/8di5_27439.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8di5_27439/02_2023/8di5_27439.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8di5_27439/02_2023/8di5_27439.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8di5_27439/02_2023/8di5_27439.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8di5_27439/02_2023/8di5_27439.pdb" } resolution = 3.04 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= -0.000 sd= 0.014 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 Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 2467 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1546 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "H" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 907 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.18, per 1000 atoms: 0.88 Number of scatterers: 2467 At special positions: 0 Unit cell: (68, 79, 73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 473 8.00 N 409 7.00 C 1573 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C1301 " - " ASN C 343 " Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 295.1 milliseconds 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 568 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 5 sheets defined 15.8% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.645A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.008A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'H' and resid 53 through 55 No H-bonds generated for 'chain 'H' and resid 53 through 55' Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.962A pdb=" N LYS H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 86 through 90 removed outlier: 4.065A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358 removed outlier: 5.268A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.296A pdb=" N GLU H 33 " --> pdb=" O VAL H 98 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N MET H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASN H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 80 hydrogen bonds defined for protein. 204 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.80 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 786 1.34 - 1.46: 698 1.46 - 1.58: 1036 1.58 - 1.70: 0 1.70 - 1.82: 14 Bond restraints: 2534 Sorted by residual: bond pdb=" CB TRP H 47 " pdb=" CG TRP H 47 " ideal model delta sigma weight residual 1.498 1.450 0.048 3.10e-02 1.04e+03 2.39e+00 bond pdb=" CB ILE C 472 " pdb=" CG2 ILE C 472 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.22e+00 bond pdb=" CB ASN H 83 " pdb=" CG ASN H 83 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.75e+00 bond pdb=" CG LEU C 452 " pdb=" CD1 LEU C 452 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.67e+00 bond pdb=" CB GLN C 493 " pdb=" CG GLN C 493 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.25e+00 ... (remaining 2529 not shown) Histogram of bond angle deviations from ideal: 101.25 - 108.03: 118 108.03 - 114.81: 1332 114.81 - 121.59: 1350 121.59 - 128.37: 630 128.37 - 135.15: 17 Bond angle restraints: 3447 Sorted by residual: angle pdb=" CA LEU C 518 " pdb=" CB LEU C 518 " pdb=" CG LEU C 518 " ideal model delta sigma weight residual 116.30 135.15 -18.85 3.50e+00 8.16e-02 2.90e+01 angle pdb=" C GLU H 33 " pdb=" N MET H 34 " pdb=" CA MET H 34 " ideal model delta sigma weight residual 122.87 118.15 4.72 1.61e+00 3.86e-01 8.60e+00 angle pdb=" C LEU C 517 " pdb=" N LEU C 518 " pdb=" CA LEU C 518 " ideal model delta sigma weight residual 122.68 126.77 -4.09 1.47e+00 4.63e-01 7.72e+00 angle pdb=" CA TYR C 495 " pdb=" CB TYR C 495 " pdb=" CG TYR C 495 " ideal model delta sigma weight residual 113.90 118.77 -4.87 1.80e+00 3.09e-01 7.31e+00 angle pdb=" CA TYR C 473 " pdb=" CB TYR C 473 " pdb=" CG TYR C 473 " ideal model delta sigma weight residual 113.90 118.55 -4.65 1.80e+00 3.09e-01 6.69e+00 ... (remaining 3442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.12: 1321 15.12 - 30.23: 128 30.23 - 45.35: 21 45.35 - 60.47: 3 60.47 - 75.58: 2 Dihedral angle restraints: 1475 sinusoidal: 574 harmonic: 901 Sorted by residual: dihedral pdb=" CA ALA C 520 " pdb=" C ALA C 520 " pdb=" N PRO C 521 " pdb=" CA PRO C 521 " ideal model delta harmonic sigma weight residual 180.00 159.25 20.75 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA LEU C 517 " pdb=" C LEU C 517 " pdb=" N LEU C 518 " pdb=" CA LEU C 518 " ideal model delta harmonic sigma weight residual 180.00 159.50 20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 95 " pdb=" CB CYS H 95 " ideal model delta sinusoidal sigma weight residual 93.00 62.46 30.54 1 1.00e+01 1.00e-02 1.33e+01 ... (remaining 1472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 209 0.038 - 0.077: 94 0.077 - 0.115: 36 0.115 - 0.154: 22 0.154 - 0.192: 3 Chirality restraints: 364 Sorted by residual: chirality pdb=" CA ILE C 434 " pdb=" N ILE C 434 " pdb=" C ILE C 434 " pdb=" CB ILE C 434 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.22e-01 chirality pdb=" CA LEU C 518 " pdb=" N LEU C 518 " pdb=" C LEU C 518 " pdb=" CB LEU C 518 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" CB THR H 90 " pdb=" CA THR H 90 " pdb=" OG1 THR H 90 " pdb=" CG2 THR H 90 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.76e-01 ... (remaining 361 not shown) Planarity restraints: 448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " -0.038 5.00e-02 4.00e+02 5.69e-02 5.18e+00 pdb=" N PRO C 521 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 462 " 0.036 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO C 463 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 463 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 463 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 362 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C VAL C 362 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL C 362 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA C 363 " -0.011 2.00e-02 2.50e+03 ... (remaining 445 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 757 2.82 - 3.34: 1959 3.34 - 3.86: 4099 3.86 - 4.38: 4610 4.38 - 4.90: 8120 Nonbonded interactions: 19545 Sorted by model distance: nonbonded pdb=" OG SER C 359 " pdb=" OD1 ASN C 394 " model vdw 2.300 2.440 nonbonded pdb=" O ASN C 481 " pdb=" NE2 GLN H 39 " model vdw 2.328 2.520 nonbonded pdb=" OD1 ASP C 442 " pdb=" OH TYR C 451 " model vdw 2.364 2.440 nonbonded pdb=" NH2 ARG C 454 " pdb=" O ASP C 467 " model vdw 2.390 2.520 nonbonded pdb=" OG SER H 117 " pdb=" N SER H 118 " model vdw 2.392 2.520 ... (remaining 19540 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: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 1573 2.51 5 N 409 2.21 5 O 473 1.98 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 14.200 Check model and map are aligned: 0.040 Process input model: 12.570 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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 : 0.006 0.049 2534 Z= 0.388 Angle : 0.946 18.847 3447 Z= 0.481 Chirality : 0.057 0.192 364 Planarity : 0.007 0.057 447 Dihedral : 12.340 75.582 892 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.41), residues: 307 helix: -4.35 (0.46), residues: 33 sheet: 0.00 (0.51), residues: 90 loop : -1.97 (0.37), residues: 184 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 0.230 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.2063 time to fit residues: 19.3642 Evaluate side-chains 68 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.269 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 437 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 2534 Z= 0.275 Angle : 0.615 11.054 3447 Z= 0.316 Chirality : 0.043 0.157 364 Planarity : 0.004 0.037 447 Dihedral : 5.189 19.375 354 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 2.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.44), residues: 307 helix: -3.42 (0.62), residues: 34 sheet: 0.18 (0.54), residues: 90 loop : -1.69 (0.40), residues: 183 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 0.268 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 73 average time/residue: 0.1946 time to fit residues: 16.1206 Evaluate side-chains 76 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 0.290 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0274 time to fit residues: 0.5754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 7 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 9 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.024 2534 Z= 0.239 Angle : 0.569 9.673 3447 Z= 0.293 Chirality : 0.042 0.147 364 Planarity : 0.004 0.034 447 Dihedral : 4.915 19.253 354 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.45), residues: 307 helix: -3.00 (0.79), residues: 34 sheet: 0.27 (0.54), residues: 89 loop : -1.59 (0.42), residues: 184 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 0.283 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 79 average time/residue: 0.2034 time to fit residues: 18.1540 Evaluate side-chains 74 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 0.261 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0316 time to fit residues: 0.4507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 0.0980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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: 0.8014 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.037 2534 Z= 0.464 Angle : 0.668 8.990 3447 Z= 0.350 Chirality : 0.045 0.149 364 Planarity : 0.004 0.035 447 Dihedral : 5.313 19.189 354 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer Outliers : 2.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.46), residues: 307 helix: -3.04 (0.78), residues: 34 sheet: 0.12 (0.53), residues: 89 loop : -1.56 (0.44), residues: 184 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.331 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 74 average time/residue: 0.2102 time to fit residues: 17.6147 Evaluate side-chains 74 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 0.320 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0265 time to fit residues: 0.6082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7976 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 2534 Z= 0.259 Angle : 0.585 8.282 3447 Z= 0.302 Chirality : 0.044 0.178 364 Planarity : 0.004 0.032 447 Dihedral : 4.941 18.929 354 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.45), residues: 307 helix: -3.03 (0.79), residues: 34 sheet: 0.16 (0.53), residues: 89 loop : -1.52 (0.43), residues: 184 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 0.321 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 75 average time/residue: 0.2009 time to fit residues: 17.0574 Evaluate side-chains 71 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 0.271 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0345 time to fit residues: 0.4685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 0.0970 chunk 13 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 21 optimal weight: 0.0870 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 2534 Z= 0.175 Angle : 0.537 7.537 3447 Z= 0.281 Chirality : 0.042 0.137 364 Planarity : 0.003 0.037 447 Dihedral : 4.687 18.334 354 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % 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: -1.47 (0.46), residues: 307 helix: -3.06 (0.92), residues: 27 sheet: 0.59 (0.56), residues: 82 loop : -1.43 (0.41), residues: 198 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.262 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.2032 time to fit residues: 16.2604 Evaluate side-chains 70 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.261 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 0.0370 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 19 optimal weight: 0.0060 chunk 14 optimal weight: 2.9990 overall best weight: 0.3874 ------------------------------------------------------------------------------- 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: 0.7942 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 2534 Z= 0.178 Angle : 0.522 7.494 3447 Z= 0.278 Chirality : 0.042 0.136 364 Planarity : 0.003 0.037 447 Dihedral : 4.548 17.895 354 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.46), residues: 307 helix: -3.17 (0.89), residues: 27 sheet: 0.61 (0.57), residues: 82 loop : -1.33 (0.42), residues: 198 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 0.293 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 77 average time/residue: 0.1999 time to fit residues: 17.4924 Evaluate side-chains 76 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 0.295 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0368 time to fit residues: 0.5903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7960 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.025 2534 Z= 0.242 Angle : 0.541 7.728 3447 Z= 0.289 Chirality : 0.043 0.136 364 Planarity : 0.003 0.038 447 Dihedral : 4.702 19.835 354 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.46), residues: 307 helix: -3.30 (0.73), residues: 34 sheet: 0.66 (0.57), residues: 82 loop : -1.28 (0.43), residues: 191 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 73 time to evaluate : 0.314 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 74 average time/residue: 0.2055 time to fit residues: 17.3815 Evaluate side-chains 73 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 0.292 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0354 time to fit residues: 0.6057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 0.0020 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.0980 chunk 29 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 18 optimal weight: 0.0980 chunk 14 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 0.3788 ------------------------------------------------------------------------------- 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: 0.7939 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 2534 Z= 0.178 Angle : 0.519 7.734 3447 Z= 0.276 Chirality : 0.042 0.137 364 Planarity : 0.003 0.037 447 Dihedral : 4.537 19.384 354 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.47), residues: 307 helix: -3.22 (0.90), residues: 27 sheet: 0.74 (0.58), residues: 82 loop : -1.32 (0.42), residues: 198 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 75 time to evaluate : 0.314 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 76 average time/residue: 0.2024 time to fit residues: 17.4554 Evaluate side-chains 75 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 0.287 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0387 time to fit residues: 0.4439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 24 optimal weight: 0.0050 chunk 4 optimal weight: 0.0980 chunk 20 optimal weight: 0.0010 chunk 1 optimal weight: 0.9990 chunk 17 optimal weight: 0.0670 overall best weight: 0.0938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 2534 Z= 0.130 Angle : 0.503 7.838 3447 Z= 0.264 Chirality : 0.042 0.136 364 Planarity : 0.003 0.041 447 Dihedral : 4.243 18.829 354 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.47), residues: 307 helix: -3.29 (0.87), residues: 27 sheet: 0.95 (0.59), residues: 82 loop : -1.30 (0.42), residues: 198 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 0.271 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 80 average time/residue: 0.2029 time to fit residues: 18.3720 Evaluate side-chains 79 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.263 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0277 time to fit residues: 0.3972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 2.9990 chunk 16 optimal weight: 0.0970 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 0.0070 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.115471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.098055 restraints weight = 4332.197| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 3.07 r_work: 0.3168 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 2534 Z= 0.205 Angle : 0.550 8.132 3447 Z= 0.283 Chirality : 0.043 0.153 364 Planarity : 0.003 0.041 447 Dihedral : 4.380 19.280 354 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % 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: -1.27 (0.47), residues: 307 helix: -3.21 (0.89), residues: 27 sheet: 0.78 (0.57), residues: 88 loop : -1.33 (0.43), residues: 192 =============================================================================== Job complete usr+sys time: 1325.95 seconds wall clock time: 24 minutes 39.96 seconds (1479.96 seconds total)