Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:38:59 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdw_23782/11_2022/7mdw_23782.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdw_23782/11_2022/7mdw_23782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdw_23782/11_2022/7mdw_23782.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdw_23782/11_2022/7mdw_23782.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdw_23782/11_2022/7mdw_23782.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdw_23782/11_2022/7mdw_23782.pdb" } resolution = 3.58 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= 0.011 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 46": "OD1" <-> "OD2" Residue "B PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 3392 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 871 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "R" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "B" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 971 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain: "R" 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: 2.44, per 1000 atoms: 0.72 Number of scatterers: 3392 At special positions: 0 Unit cell: (57.5916, 79.4066, 107.33, 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 15 16.00 O 652 8.00 N 587 7.00 C 2138 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.03 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.03 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " 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 R 601 " - " ASN R 343 " Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 472.3 milliseconds 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 784 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 9 sheets defined 8.5% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'R' and resid 337 through 343 Processing helix chain 'R' and resid 365 through 370 removed outlier: 3.685A pdb=" N ASN R 370 " --> pdb=" O SER R 366 " (cutoff:3.500A) Processing helix chain 'R' and resid 385 through 390 Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'B' and resid 27 through 32 removed outlier: 4.388A pdb=" N SER B 30 " --> pdb=" O ARG B 27 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 45 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 49 Processing sheet with id=AA3, first strand: chain 'A' and resid 70 through 71 Processing sheet with id=AA4, first strand: chain 'R' and resid 354 through 358 removed outlier: 4.199A pdb=" N ASN R 354 " --> pdb=" O SER R 399 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER R 399 " --> pdb=" O ASN R 354 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL R 395 " --> pdb=" O ILE R 358 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN R 394 " --> pdb=" O GLU R 516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'R' and resid 361 through 362 removed outlier: 7.585A pdb=" N CYS R 361 " --> pdb=" O CYS R 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'R' and resid 448 through 454 removed outlier: 4.340A pdb=" N ASN R 450 " --> pdb=" O TYR R 495 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N TYR R 495 " --> pdb=" O ASN R 450 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LEU R 452 " --> pdb=" O GLN R 493 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLN R 493 " --> pdb=" O LEU R 452 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 473 through 474 Processing sheet with id=AA8, first strand: chain 'B' and resid 5 through 7 removed outlier: 3.977A pdb=" N VAL B 5 " --> pdb=" O ALA B 23 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER B 7 " --> pdb=" O SER B 21 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER B 21 " --> pdb=" O SER B 7 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 58 through 60 removed outlier: 6.510A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N THR B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N MET B 34 " --> pdb=" O THR B 50 " (cutoff:3.500A) 63 hydrogen bonds defined for protein. 141 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: 0.77 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1112 1.34 - 1.46: 899 1.46 - 1.58: 1440 1.58 - 1.70: 0 1.70 - 1.81: 18 Bond restraints: 3469 Sorted by residual: bond pdb=" CA ILE R 410 " pdb=" CB ILE R 410 " ideal model delta sigma weight residual 1.527 1.540 -0.013 1.31e-02 5.83e+03 9.96e-01 bond pdb=" N PRO B 41 " pdb=" CA PRO B 41 " ideal model delta sigma weight residual 1.468 1.474 -0.006 7.90e-03 1.60e+04 6.17e-01 bond pdb=" CA THR A 105 " pdb=" CB THR A 105 " ideal model delta sigma weight residual 1.534 1.546 -0.012 1.65e-02 3.67e+03 5.03e-01 bond pdb=" CB TYR R 495 " pdb=" CG TYR R 495 " ideal model delta sigma weight residual 1.512 1.498 0.014 2.20e-02 2.07e+03 4.26e-01 bond pdb=" C PHE A 66 " pdb=" O PHE A 66 " ideal model delta sigma weight residual 1.235 1.227 0.008 1.26e-02 6.30e+03 4.06e-01 ... (remaining 3464 not shown) Histogram of bond angle deviations from ideal: 100.84 - 107.46: 77 107.46 - 114.09: 1847 114.09 - 120.72: 1402 120.72 - 127.34: 1355 127.34 - 133.97: 27 Bond angle restraints: 4708 Sorted by residual: angle pdb=" N GLY R 496 " pdb=" CA GLY R 496 " pdb=" C GLY R 496 " ideal model delta sigma weight residual 111.19 117.79 -6.60 1.75e+00 3.27e-01 1.42e+01 angle pdb=" C ASN A 82 " pdb=" N SER A 83 " pdb=" CA SER A 83 " ideal model delta sigma weight residual 121.54 125.96 -4.42 1.91e+00 2.74e-01 5.36e+00 angle pdb=" CA THR A 105 " pdb=" CB THR A 105 " pdb=" CG2 THR A 105 " ideal model delta sigma weight residual 110.50 114.38 -3.88 1.70e+00 3.46e-01 5.22e+00 angle pdb=" N VAL A 2 " pdb=" CA VAL A 2 " pdb=" C VAL A 2 " ideal model delta sigma weight residual 111.48 109.38 2.10 9.40e-01 1.13e+00 5.00e+00 angle pdb=" C PHE A 66 " pdb=" CA PHE A 66 " pdb=" CB PHE A 66 " ideal model delta sigma weight residual 110.42 114.77 -4.35 1.99e+00 2.53e-01 4.79e+00 ... (remaining 4703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 1859 17.94 - 35.88: 141 35.88 - 53.82: 20 53.82 - 71.77: 3 71.77 - 89.71: 2 Dihedral angle restraints: 2025 sinusoidal: 780 harmonic: 1245 Sorted by residual: dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 94 " pdb=" CB CYS A 94 " ideal model delta sinusoidal sigma weight residual -86.00 -140.97 54.97 1 1.00e+01 1.00e-02 4.09e+01 dihedral pdb=" CA THR A 105 " pdb=" C THR A 105 " pdb=" N TYR A 106 " pdb=" CA TYR A 106 " ideal model delta harmonic sigma weight residual 180.00 153.80 26.20 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA ASP B 46 " pdb=" CB ASP B 46 " pdb=" CG ASP B 46 " pdb=" OD1 ASP B 46 " ideal model delta sinusoidal sigma weight residual -30.00 -88.19 58.19 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 2022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 374 0.039 - 0.079: 89 0.079 - 0.118: 42 0.118 - 0.157: 0 0.157 - 0.196: 1 Chirality restraints: 506 Sorted by residual: chirality pdb=" CB THR A 105 " pdb=" CA THR A 105 " pdb=" OG1 THR A 105 " pdb=" CG2 THR A 105 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.20 2.00e-01 2.50e+01 9.62e-01 chirality pdb=" CA ILE A 68 " pdb=" N ILE A 68 " pdb=" C ILE A 68 " pdb=" CB ILE A 68 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.45e-01 chirality pdb=" CA ILE R 468 " pdb=" N ILE R 468 " pdb=" C ILE R 468 " pdb=" CB ILE R 468 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.25e-01 ... (remaining 503 not shown) Planarity restraints: 615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE R 490 " -0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO R 491 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO R 491 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO R 491 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 104 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.79e+00 pdb=" C TYR A 104 " -0.023 2.00e-02 2.50e+03 pdb=" O TYR A 104 " 0.009 2.00e-02 2.50e+03 pdb=" N THR A 105 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 34 " -0.002 2.00e-02 2.50e+03 7.83e-03 1.53e+00 pdb=" CG TRP A 34 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP A 34 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 34 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 34 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 34 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 34 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 34 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 34 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 34 " 0.000 2.00e-02 2.50e+03 ... (remaining 612 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1006 2.81 - 3.34: 2901 3.34 - 3.86: 5326 3.86 - 4.38: 6065 4.38 - 4.90: 10459 Nonbonded interactions: 25757 Sorted by model distance: nonbonded pdb=" ND2 ASN A 52 " pdb=" O TYR R 449 " model vdw 2.293 2.520 nonbonded pdb=" OD2 ASP R 398 " pdb=" OH TYR R 423 " model vdw 2.359 2.440 nonbonded pdb=" OG SER R 477 " pdb=" OD1 ASN R 487 " model vdw 2.367 2.440 nonbonded pdb=" OH TYR R 365 " pdb=" O PRO R 384 " model vdw 2.372 2.440 nonbonded pdb=" NH2 ARG R 357 " pdb=" OD1 ASN R 394 " model vdw 2.380 2.520 ... (remaining 25752 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 15 5.16 5 C 2138 2.51 5 N 587 2.21 5 O 652 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=0.50 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: 2.010 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: 9.260 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.030 Process input model: 14.940 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4435 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 : 0.002 0.031 3469 Z= 0.127 Angle : 0.539 6.596 4708 Z= 0.309 Chirality : 0.041 0.196 506 Planarity : 0.003 0.043 614 Dihedral : 12.633 89.707 1223 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % 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: -1.58 (0.38), residues: 429 helix: -1.98 (0.79), residues: 39 sheet: -0.34 (0.53), residues: 98 loop : -1.21 (0.34), residues: 292 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.353 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1839 time to fit residues: 4.8728 Evaluate side-chains 20 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.371 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.5980 chunk 31 optimal weight: 0.0670 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 24 optimal weight: 0.0010 chunk 38 optimal weight: 0.7980 chunk 11 optimal weight: 0.0170 overall best weight: 0.2762 ------------------------------------------------------------------------------- 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: 0.4535 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 3469 Z= 0.174 Angle : 0.533 7.233 4708 Z= 0.286 Chirality : 0.043 0.168 506 Planarity : 0.003 0.039 614 Dihedral : 5.974 88.955 496 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer Outliers : 0.28 % 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: -1.86 (0.38), residues: 429 helix: -1.90 (0.72), residues: 45 sheet: -0.95 (0.51), residues: 93 loop : -1.25 (0.34), residues: 291 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.361 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 20 average time/residue: 0.1741 time to fit residues: 4.6698 Evaluate side-chains 21 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.363 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0382 time to fit residues: 0.5711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 41 optimal weight: 0.4980 chunk 34 optimal weight: 0.7980 chunk 37 optimal weight: 0.2980 chunk 13 optimal weight: 0.9990 chunk 30 optimal weight: 0.0970 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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: 0.4706 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 3469 Z= 0.243 Angle : 0.591 6.448 4708 Z= 0.320 Chirality : 0.044 0.158 506 Planarity : 0.004 0.048 614 Dihedral : 6.595 87.208 496 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.34 (0.38), residues: 429 helix: -2.34 (0.65), residues: 45 sheet: -1.29 (0.50), residues: 101 loop : -1.56 (0.35), residues: 283 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 18 time to evaluate : 0.319 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 19 average time/residue: 0.1298 time to fit residues: 3.6667 Evaluate side-chains 18 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.353 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 0.4980 chunk 25 optimal weight: 0.8980 chunk 38 optimal weight: 0.1980 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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: 0.4777 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 3469 Z= 0.234 Angle : 0.594 6.510 4708 Z= 0.322 Chirality : 0.045 0.159 506 Planarity : 0.004 0.037 614 Dihedral : 6.817 86.481 496 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.65 (0.37), residues: 429 helix: -2.75 (0.68), residues: 40 sheet: -1.57 (0.50), residues: 101 loop : -1.75 (0.34), residues: 288 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 20 time to evaluate : 0.335 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 25 average time/residue: 0.1133 time to fit residues: 4.0085 Evaluate side-chains 24 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 20 time to evaluate : 0.355 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0420 time to fit residues: 0.8024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 0.0010 chunk 34 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 0.0060 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 23 optimal weight: 0.3980 overall best weight: 0.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4744 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 3469 Z= 0.181 Angle : 0.556 6.301 4708 Z= 0.299 Chirality : 0.044 0.190 506 Planarity : 0.003 0.033 614 Dihedral : 6.540 86.571 496 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.69 (0.38), residues: 429 helix: -2.80 (0.66), residues: 40 sheet: -1.73 (0.50), residues: 101 loop : -1.71 (0.35), residues: 288 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 20 time to evaluate : 0.365 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 21 average time/residue: 0.1298 time to fit residues: 3.9476 Evaluate side-chains 21 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 19 time to evaluate : 0.363 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0352 time to fit residues: 0.6616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 18 optimal weight: 0.0070 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 0.0980 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.0980 overall best weight: 0.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4762 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 3469 Z= 0.178 Angle : 0.555 6.541 4708 Z= 0.298 Chirality : 0.044 0.186 506 Planarity : 0.003 0.033 614 Dihedral : 6.524 86.857 496 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.73 (0.38), residues: 429 helix: -2.80 (0.67), residues: 40 sheet: -1.73 (0.50), residues: 99 loop : -1.77 (0.35), residues: 290 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.357 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 20 average time/residue: 0.1287 time to fit residues: 3.7588 Evaluate side-chains 21 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.361 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0357 time to fit residues: 0.6005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.9990 chunk 34 optimal weight: 0.0040 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 0.0070 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 0.2980 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 0.0270 overall best weight: 0.2468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4738 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 3469 Z= 0.159 Angle : 0.538 6.651 4708 Z= 0.289 Chirality : 0.043 0.191 506 Planarity : 0.003 0.032 614 Dihedral : 6.370 86.981 496 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.68 (0.38), residues: 429 helix: -2.79 (0.67), residues: 40 sheet: -1.72 (0.50), residues: 99 loop : -1.71 (0.35), residues: 290 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 20 time to evaluate : 0.276 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 22 average time/residue: 0.1509 time to fit residues: 4.4463 Evaluate side-chains 21 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.352 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4420 time to fit residues: 0.9925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 36 optimal weight: 0.0980 chunk 38 optimal weight: 0.4980 chunk 35 optimal weight: 0.1980 chunk 37 optimal weight: 0.0980 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 0.0870 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 0.0020 chunk 34 optimal weight: 0.0770 overall best weight: 0.0724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4638 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 3469 Z= 0.120 Angle : 0.500 7.308 4708 Z= 0.264 Chirality : 0.042 0.186 506 Planarity : 0.003 0.032 614 Dihedral : 5.933 87.451 496 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer Outliers : 0.85 % 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: -2.56 (0.38), residues: 429 helix: -2.72 (0.68), residues: 40 sheet: -1.70 (0.49), residues: 101 loop : -1.60 (0.35), residues: 288 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 21 time to evaluate : 0.391 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 23 average time/residue: 0.1239 time to fit residues: 4.0947 Evaluate side-chains 22 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 20 time to evaluate : 0.343 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0334 time to fit residues: 0.6348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 24 optimal weight: 0.4980 chunk 39 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 41 optimal weight: 0.0980 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4810 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 3469 Z= 0.232 Angle : 0.589 8.138 4708 Z= 0.318 Chirality : 0.045 0.192 506 Planarity : 0.004 0.031 614 Dihedral : 6.709 87.105 496 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.72 (0.38), residues: 429 helix: -2.83 (0.67), residues: 40 sheet: -1.78 (0.49), residues: 99 loop : -1.72 (0.35), residues: 290 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 20 time to evaluate : 0.365 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 21 average time/residue: 0.1333 time to fit residues: 4.0783 Evaluate side-chains 21 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.358 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0343 time to fit residues: 0.5887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.1980 chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 30 optimal weight: 0.1980 chunk 4 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 13 optimal weight: 0.0670 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 0.0980 overall best weight: 0.2118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4737 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 3469 Z= 0.152 Angle : 0.527 8.277 4708 Z= 0.281 Chirality : 0.043 0.176 506 Planarity : 0.003 0.032 614 Dihedral : 6.332 87.580 496 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.67 (0.38), residues: 429 helix: -2.79 (0.69), residues: 40 sheet: -1.69 (0.51), residues: 99 loop : -1.71 (0.34), residues: 290 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.329 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1160 time to fit residues: 3.5410 Evaluate side-chains 21 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.309 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.4980 chunk 1 optimal weight: 0.0070 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.0670 chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 0.0030 chunk 15 optimal weight: 0.0170 chunk 41 optimal weight: 0.0970 overall best weight: 0.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4839 r_free = 0.4839 target = 0.236360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.229403 restraints weight = 5625.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.230482 restraints weight = 4536.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.231392 restraints weight = 3691.837| |-----------------------------------------------------------------------------| r_work (final): 0.4786 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4839 r_free = 0.4839 target_work(ls_wunit_k1) = 0.236 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4837 r_free = 0.4837 target_work(ls_wunit_k1) = 0.236 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4620 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 3469 Z= 0.119 Angle : 0.493 7.316 4708 Z= 0.259 Chirality : 0.042 0.186 506 Planarity : 0.003 0.033 614 Dihedral : 5.793 87.739 496 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer Outliers : 0.28 % 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: -2.34 (0.39), residues: 429 helix: -2.37 (0.81), residues: 34 sheet: -1.55 (0.50), residues: 101 loop : -1.50 (0.35), residues: 294 =============================================================================== Job complete usr+sys time: 1271.26 seconds wall clock time: 23 minutes 55.17 seconds (1435.17 seconds total)