Starting phenix.real_space_refine (version: dev) on Fri Feb 17 04:52:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdw_23782/02_2023/7mdw_23782.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdw_23782/02_2023/7mdw_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_23782/02_2023/7mdw_23782.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdw_23782/02_2023/7mdw_23782.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdw_23782/02_2023/7mdw_23782.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdw_23782/02_2023/7mdw_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 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-4877/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: 2.48, per 1000 atoms: 0.73 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: 1.22 Conformation dependent library (CDL) restraints added in 539.0 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: 0.20 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: 0.76 Time building geometry restraints manager: 1.35 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: 2.840 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: 9.940 Check model and map are aligned: 0.050 Process input model: 13.420 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.210 ------------------------------------------------------------------------------- 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 : 0.340 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1900 time to fit residues: 4.9868 Evaluate side-chains 20 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.381 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5595 ------------------------------------------------------------------------------- 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: 0.0040 chunk 38 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 overall best weight: 0.4330 ------------------------------------------------------------------------------- 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: 0.4629 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 3469 Z= 0.236 Angle : 0.586 8.001 4708 Z= 0.317 Chirality : 0.044 0.171 506 Planarity : 0.004 0.039 614 Dihedral : 6.287 88.193 496 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % 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: -2.02 (0.38), residues: 429 helix: -2.06 (0.70), residues: 45 sheet: -1.13 (0.51), residues: 93 loop : -1.33 (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 : 0.360 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 20 average time/residue: 0.1861 time to fit residues: 4.9077 Evaluate side-chains 21 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.355 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0360 time to fit residues: 0.5889 ------------------------------------------------------------------------------- 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: 0.8980 chunk 25 optimal weight: 0.3980 chunk 10 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 28 optimal weight: 0.0670 chunk 19 optimal weight: 0.4980 overall best weight: 0.4318 ------------------------------------------------------------------------------- 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: 0.4715 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 3469 Z= 0.230 Angle : 0.585 6.603 4708 Z= 0.316 Chirality : 0.044 0.154 506 Planarity : 0.004 0.058 614 Dihedral : 6.588 87.100 496 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer Outliers : 1.13 % 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: -2.40 (0.37), residues: 429 helix: -2.60 (0.70), residues: 39 sheet: -1.37 (0.50), residues: 101 loop : -1.58 (0.34), residues: 289 *********************** 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 22 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 18 time to evaluate : 0.367 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 20 average time/residue: 0.1346 time to fit residues: 3.9824 Evaluate side-chains 20 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 18 time to evaluate : 0.358 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0359 time to fit residues: 0.6589 ------------------------------------------------------------------------------- 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: 0.7980 chunk 18 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 38 optimal weight: 0.0980 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 0.0040 chunk 36 optimal weight: 0.0060 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 overall best weight: 0.2408 ------------------------------------------------------------------------------- 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: 0.4675 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 3469 Z= 0.158 Angle : 0.525 5.846 4708 Z= 0.279 Chirality : 0.043 0.146 506 Planarity : 0.003 0.030 614 Dihedral : 6.238 87.178 496 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer Outliers : 1.41 % 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: -2.44 (0.38), residues: 429 helix: -2.43 (0.64), residues: 45 sheet: -1.39 (0.51), residues: 99 loop : -1.61 (0.35), residues: 285 *********************** 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 23 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 18 time to evaluate : 0.364 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 22 average time/residue: 0.1338 time to fit residues: 4.2441 Evaluate side-chains 19 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 17 time to evaluate : 0.348 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0444 time to fit residues: 0.6680 ------------------------------------------------------------------------------- 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: 0.0170 chunk 34 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.4875 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 3469 Z= 0.332 Angle : 0.703 7.915 4708 Z= 0.383 Chirality : 0.048 0.177 506 Planarity : 0.005 0.044 614 Dihedral : 7.356 85.698 496 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.42 % Favored : 88.58 % Rotamer Outliers : 1.41 % 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: -2.90 (0.37), residues: 429 helix: -2.95 (0.65), residues: 40 sheet: -1.85 (0.47), residues: 112 loop : -1.85 (0.35), residues: 277 *********************** 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 25 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 20 time to evaluate : 0.356 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 22 average time/residue: 0.1265 time to fit residues: 3.9921 Evaluate side-chains 24 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 20 time to evaluate : 0.349 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0360 time to fit residues: 0.7987 ------------------------------------------------------------------------------- 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: 0.8980 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 18 optimal weight: 0.2980 chunk 3 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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: 0.4850 moved from start: 0.3327 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= 0.251 Angle : 0.624 6.923 4708 Z= 0.339 Chirality : 0.046 0.192 506 Planarity : 0.004 0.035 614 Dihedral : 7.082 85.254 496 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % 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: -2.98 (0.37), residues: 429 helix: -2.89 (0.68), residues: 40 sheet: -1.96 (0.49), residues: 101 loop : -1.92 (0.34), residues: 288 *********************** 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 : 0.354 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 21 average time/residue: 0.1623 time to fit residues: 4.5529 Evaluate side-chains 21 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.305 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4250 time to fit residues: 0.9034 ------------------------------------------------------------------------------- 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: 0.0870 chunk 34 optimal weight: 0.0870 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 0.0570 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 27 optimal weight: 0.0770 chunk 20 optimal weight: 0.2980 overall best weight: 0.1212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 474 GLN R 481 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4696 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 3469 Z= 0.131 Angle : 0.525 5.992 4708 Z= 0.278 Chirality : 0.043 0.193 506 Planarity : 0.003 0.037 614 Dihedral : 6.211 84.906 496 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % 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: -2.73 (0.38), residues: 429 helix: -2.70 (0.71), residues: 40 sheet: -1.81 (0.50), residues: 99 loop : -1.75 (0.34), 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: 3 poor density : 19 time to evaluate : 0.364 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 22 average time/residue: 0.1287 time to fit residues: 4.1778 Evaluate side-chains 21 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 19 time to evaluate : 0.414 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0418 time to fit residues: 0.7523 ------------------------------------------------------------------------------- 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: 0.9990 chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 0.0570 chunk 16 optimal weight: 0.1980 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 0.0000 chunk 34 optimal weight: 0.4980 overall best weight: 0.2702 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4764 moved from start: 0.3174 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= 0.169 Angle : 0.553 8.100 4708 Z= 0.294 Chirality : 0.043 0.199 506 Planarity : 0.003 0.034 614 Dihedral : 6.406 86.274 496 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.76 (0.38), residues: 429 helix: -2.78 (0.69), residues: 40 sheet: -1.81 (0.50), residues: 99 loop : -1.76 (0.34), residues: 290 *********************** 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 25 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 22 time to evaluate : 0.351 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 24 average time/residue: 0.1270 time to fit residues: 4.3229 Evaluate side-chains 23 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.321 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0379 time to fit residues: 0.6042 ------------------------------------------------------------------------------- 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: 1.9990 chunk 24 optimal weight: 0.1980 chunk 39 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4877 moved from start: 0.3635 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= 0.274 Angle : 0.645 8.428 4708 Z= 0.348 Chirality : 0.046 0.196 506 Planarity : 0.004 0.032 614 Dihedral : 7.143 85.928 496 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.19 % Favored : 88.81 % 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: -3.01 (0.37), residues: 429 helix: -2.94 (0.68), residues: 40 sheet: -2.00 (0.49), residues: 99 loop : -1.94 (0.34), 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 : 0.339 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 22 average time/residue: 0.1360 time to fit residues: 4.2098 Evaluate side-chains 21 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.346 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0554 time to fit residues: 0.6220 ------------------------------------------------------------------------------- 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: 0.5980 chunk 26 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 chunk 30 optimal weight: 0.4980 chunk 4 optimal weight: 0.7980 chunk 9 optimal weight: 0.0870 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 0.0980 chunk 34 optimal weight: 0.3980 chunk 6 optimal weight: 0.1980 overall best weight: 0.1958 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4760 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 3469 Z= 0.150 Angle : 0.548 8.293 4708 Z= 0.290 Chirality : 0.043 0.189 506 Planarity : 0.003 0.035 614 Dihedral : 6.418 86.339 496 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 16.01 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 : 0.24 % 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: -2.86 (0.37), residues: 429 helix: -2.84 (0.69), residues: 40 sheet: -1.94 (0.49), residues: 101 loop : -1.81 (0.34), residues: 288 ********************** 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: 1 poor density : 20 time to evaluate : 0.275 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 21 average time/residue: 0.1229 time to fit residues: 3.7324 Evaluate side-chains 20 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.334 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5202 ------------------------------------------------------------------------------- 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: 0.6980 chunk 1 optimal weight: 0.0470 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.2980 chunk 41 optimal weight: 0.9980 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.225687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.212374 restraints weight = 5340.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.215318 restraints weight = 3610.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.217148 restraints weight = 2600.882| |-----------------------------------------------------------------------------| r_work (final): 0.4643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4732 r_free = 0.4732 target_work(ls_wunit_k1) = 0.226 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4731 r_free = 0.4731 target_work(ls_wunit_k1) = 0.226 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4940 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 3469 Z= 0.245 Angle : 0.619 8.252 4708 Z= 0.333 Chirality : 0.046 0.203 506 Planarity : 0.004 0.032 614 Dihedral : 6.937 86.596 496 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.89 % Favored : 88.11 % 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: -3.01 (0.37), residues: 429 helix: -2.92 (0.67), residues: 40 sheet: -1.95 (0.49), residues: 99 loop : -1.97 (0.34), residues: 290 =============================================================================== Job complete usr+sys time: 1272.12 seconds wall clock time: 23 minutes 46.85 seconds (1426.85 seconds total)