Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 01:01:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr0_34041/04_2023/7yr0_34041.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr0_34041/04_2023/7yr0_34041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr0_34041/04_2023/7yr0_34041.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr0_34041/04_2023/7yr0_34041.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr0_34041/04_2023/7yr0_34041.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr0_34041/04_2023/7yr0_34041.pdb" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2149 2.51 5 N 571 2.21 5 O 648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 3383 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1560 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 183} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 959 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "B" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 815 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.45, per 1000 atoms: 0.72 Number of scatterers: 3383 At special positions: 0 Unit cell: (73.83, 85.6, 81.32, 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 648 8.00 N 571 7.00 C 2149 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 89 " 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " BETA1-6 " NAG D 1 " - " FUC D 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG D 1 " - " ASN A 343 " Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 500.8 milliseconds 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 774 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 8 sheets defined 6.3% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.995A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 337 through 342' Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.799A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'C' and resid 61 through 65 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.310A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.597A pdb=" N TYR A 453 " --> pdb=" O GLN A 493 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AA4, first strand: chain 'C' and resid 49 through 51 removed outlier: 3.890A pdb=" N GLY C 33 " --> pdb=" O ASP C 99 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ASN C 116 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 49 through 51 removed outlier: 3.890A pdb=" N GLY C 33 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 11 removed outlier: 3.697A pdb=" N LEU B 11 " --> pdb=" O LYS B 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 19 through 22 removed outlier: 3.763A pdb=" N ASP B 71 " --> pdb=" O SER B 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 46 through 47 removed outlier: 4.117A pdb=" N THR B 97 " --> pdb=" O GLN B 91 " (cutoff:3.500A) 82 hydrogen bonds defined for protein. 189 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: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1073 1.35 - 1.46: 942 1.46 - 1.58: 1439 1.58 - 1.70: 0 1.70 - 1.82: 18 Bond restraints: 3472 Sorted by residual: bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.547 -0.028 2.00e-02 2.50e+03 1.96e+00 bond pdb=" C2 NAG D 2 " pdb=" N2 NAG D 2 " ideal model delta sigma weight residual 1.439 1.464 -0.025 2.00e-02 2.50e+03 1.58e+00 bond pdb=" CA GLY A 381 " pdb=" C GLY A 381 " ideal model delta sigma weight residual 1.512 1.523 -0.011 8.70e-03 1.32e+04 1.56e+00 bond pdb=" C5 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.413 1.437 -0.024 2.00e-02 2.50e+03 1.38e+00 bond pdb=" C5 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.36e+00 ... (remaining 3467 not shown) Histogram of bond angle deviations from ideal: 100.55 - 107.25: 117 107.25 - 113.94: 1840 113.94 - 120.63: 1324 120.63 - 127.33: 1402 127.33 - 134.02: 37 Bond angle restraints: 4720 Sorted by residual: angle pdb=" N ILE A 402 " pdb=" CA ILE A 402 " pdb=" C ILE A 402 " ideal model delta sigma weight residual 108.53 111.81 -3.28 1.22e+00 6.72e-01 7.23e+00 angle pdb=" C GLU C 82 " pdb=" CA GLU C 82 " pdb=" CB GLU C 82 " ideal model delta sigma weight residual 110.42 115.40 -4.98 1.99e+00 2.53e-01 6.25e+00 angle pdb=" C GLU B 80 " pdb=" CA GLU B 80 " pdb=" CB GLU B 80 " ideal model delta sigma weight residual 109.26 112.83 -3.57 1.47e+00 4.63e-01 5.91e+00 angle pdb=" C MET C 48 " pdb=" N GLY C 49 " pdb=" CA GLY C 49 " ideal model delta sigma weight residual 121.46 119.21 2.25 9.50e-01 1.11e+00 5.63e+00 angle pdb=" N GLY C 49 " pdb=" CA GLY C 49 " pdb=" C GLY C 49 " ideal model delta sigma weight residual 110.90 114.36 -3.46 1.53e+00 4.27e-01 5.12e+00 ... (remaining 4715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 1787 17.67 - 35.35: 177 35.35 - 53.02: 28 53.02 - 70.69: 2 70.69 - 88.36: 4 Dihedral angle restraints: 1998 sinusoidal: 773 harmonic: 1225 Sorted by residual: dihedral pdb=" CA SER B 7 " pdb=" C SER B 7 " pdb=" N PRO B 8 " pdb=" CA PRO B 8 " ideal model delta harmonic sigma weight residual 180.00 154.07 25.93 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 54.67 38.33 1 1.00e+01 1.00e-02 2.07e+01 dihedral pdb=" CA TYR C 80 " pdb=" C TYR C 80 " pdb=" N MET C 81 " pdb=" CA MET C 81 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 1995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 448 0.066 - 0.133: 61 0.133 - 0.199: 4 0.199 - 0.265: 0 0.265 - 0.331: 2 Chirality restraints: 515 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C2 NAG D 2 " pdb=" C1 NAG D 2 " pdb=" C3 NAG D 2 " pdb=" N2 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.31 -0.19 2.00e-01 2.50e+01 8.59e-01 ... (remaining 512 not shown) Planarity restraints: 606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 7 " -0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO B 8 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 8 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 8 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP C 47 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.35e+00 pdb=" C TRP C 47 " -0.020 2.00e-02 2.50e+03 pdb=" O TRP C 47 " 0.008 2.00e-02 2.50e+03 pdb=" N MET C 48 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 47 " 0.009 2.00e-02 2.50e+03 7.14e-03 1.27e+00 pdb=" CG TRP C 47 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TRP C 47 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP C 47 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 47 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 47 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 47 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 47 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 47 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 47 " 0.001 2.00e-02 2.50e+03 ... (remaining 603 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 130 2.71 - 3.26: 3238 3.26 - 3.81: 5061 3.81 - 4.35: 6100 4.35 - 4.90: 10380 Nonbonded interactions: 24909 Sorted by model distance: nonbonded pdb=" OG1 THR C 69 " pdb=" OE2 GLU C 82 " model vdw 2.164 2.440 nonbonded pdb=" O VAL B 3 " pdb=" OG SER B 26 " model vdw 2.229 2.440 nonbonded pdb=" OG SER C 35 " pdb=" OD2 ASP C 99 " model vdw 2.250 2.440 nonbonded pdb=" NH1 ARG C 87 " pdb=" OD1 ASP C 89 " model vdw 2.253 2.520 nonbonded pdb=" O ALA A 419 " pdb=" NZ LYS A 424 " model vdw 2.259 2.520 ... (remaining 24904 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.010 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: 9.630 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.730 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 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 : 0.003 0.028 3472 Z= 0.204 Angle : 0.681 6.280 4720 Z= 0.347 Chirality : 0.049 0.331 515 Planarity : 0.004 0.034 605 Dihedral : 13.750 88.364 1209 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.31 % Favored : 91.45 % 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: -1.76 (0.43), residues: 421 helix: -0.21 (3.10), residues: 6 sheet: 0.50 (0.59), residues: 92 loop : -1.86 (0.35), residues: 323 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.371 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1696 time to fit residues: 15.3535 Evaluate side-chains 57 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.362 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 4.9990 chunk 31 optimal weight: 0.0270 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.0570 chunk 37 optimal weight: 4.9990 overall best weight: 0.8958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 3472 Z= 0.220 Angle : 0.624 9.237 4720 Z= 0.309 Chirality : 0.045 0.262 515 Planarity : 0.004 0.034 605 Dihedral : 4.620 25.394 474 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.74 % Favored : 90.02 % Rotamer Outliers : 1.69 % 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: -1.89 (0.42), residues: 421 helix: -2.10 (1.61), residues: 12 sheet: 0.27 (0.58), residues: 98 loop : -1.89 (0.35), residues: 311 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 0.384 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 66 average time/residue: 0.1603 time to fit residues: 13.0242 Evaluate side-chains 60 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.395 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0407 time to fit residues: 0.7947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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: 0.7792 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 3472 Z= 0.264 Angle : 0.650 9.525 4720 Z= 0.319 Chirality : 0.045 0.239 515 Planarity : 0.004 0.033 605 Dihedral : 4.689 25.524 474 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.45 % Favored : 89.31 % Rotamer Outliers : 1.40 % 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: -1.97 (0.41), residues: 421 helix: -1.96 (1.23), residues: 20 sheet: 0.33 (0.58), residues: 98 loop : -1.99 (0.35), residues: 303 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.372 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 67 average time/residue: 0.1605 time to fit residues: 13.1924 Evaluate side-chains 61 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.401 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0360 time to fit residues: 0.7309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 39 optimal weight: 0.0980 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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: 0.7763 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 3472 Z= 0.193 Angle : 0.623 9.548 4720 Z= 0.304 Chirality : 0.045 0.252 515 Planarity : 0.003 0.033 605 Dihedral : 4.520 25.397 474 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.50 % Favored : 90.26 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.90 (0.41), residues: 421 helix: -1.99 (1.23), residues: 20 sheet: 0.33 (0.58), residues: 98 loop : -1.91 (0.35), residues: 303 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 0.400 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 70 average time/residue: 0.1646 time to fit residues: 14.2657 Evaluate side-chains 66 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.405 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0430 time to fit residues: 0.9794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 0.1980 chunk 35 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 0.0980 chunk 7 optimal weight: 0.7980 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: 0.7735 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 3472 Z= 0.166 Angle : 0.617 9.572 4720 Z= 0.298 Chirality : 0.044 0.244 515 Planarity : 0.003 0.033 605 Dihedral : 4.439 25.157 474 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.55 % Favored : 91.21 % Rotamer Outliers : 1.40 % 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: -1.82 (0.41), residues: 421 helix: -2.02 (1.22), residues: 20 sheet: 0.38 (0.58), residues: 98 loop : -1.84 (0.35), residues: 303 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.378 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 68 average time/residue: 0.1674 time to fit residues: 13.8099 Evaluate side-chains 60 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.393 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0332 time to fit residues: 0.5861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 3472 Z= 0.199 Angle : 0.623 9.596 4720 Z= 0.301 Chirality : 0.043 0.235 515 Planarity : 0.003 0.032 605 Dihedral : 4.414 24.763 474 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.26 % Favored : 90.50 % Rotamer Outliers : 2.53 % 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: -1.85 (0.41), residues: 421 helix: -2.03 (1.23), residues: 20 sheet: 0.46 (0.57), residues: 95 loop : -1.89 (0.35), residues: 306 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 0.388 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 67 average time/residue: 0.1675 time to fit residues: 13.7843 Evaluate side-chains 64 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.409 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0730 time to fit residues: 1.1546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 0.2980 chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 0.4980 chunk 11 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7757 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 3472 Z= 0.187 Angle : 0.609 9.671 4720 Z= 0.296 Chirality : 0.043 0.252 515 Planarity : 0.003 0.032 605 Dihedral : 4.397 24.442 474 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.31 % Favored : 91.45 % Rotamer Outliers : 1.12 % 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: -1.80 (0.41), residues: 421 helix: -2.03 (1.22), residues: 20 sheet: 0.50 (0.57), residues: 95 loop : -1.85 (0.35), residues: 306 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 0.422 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 62 average time/residue: 0.1714 time to fit residues: 12.9995 Evaluate side-chains 59 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.398 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0353 time to fit residues: 0.6008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 35 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 16 optimal weight: 0.3980 chunk 28 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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: 0.7766 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 3472 Z= 0.187 Angle : 0.630 9.517 4720 Z= 0.306 Chirality : 0.043 0.237 515 Planarity : 0.003 0.032 605 Dihedral : 4.319 24.246 474 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.26 % Favored : 90.50 % Rotamer Outliers : 1.97 % 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: -1.72 (0.42), residues: 421 helix: -2.02 (1.22), residues: 20 sheet: 0.59 (0.57), residues: 95 loop : -1.80 (0.35), residues: 306 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.416 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 62 average time/residue: 0.1719 time to fit residues: 13.0182 Evaluate side-chains 59 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.387 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0352 time to fit residues: 0.6757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 9.9990 chunk 33 optimal weight: 0.0870 chunk 34 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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: 0.7759 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 3472 Z= 0.184 Angle : 0.635 9.533 4720 Z= 0.312 Chirality : 0.043 0.240 515 Planarity : 0.003 0.032 605 Dihedral : 4.290 22.806 474 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.08 % Favored : 91.69 % 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: -1.69 (0.42), residues: 421 helix: -2.04 (1.22), residues: 20 sheet: 0.65 (0.58), residues: 95 loop : -1.79 (0.35), residues: 306 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.436 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 58 average time/residue: 0.1828 time to fit residues: 13.0021 Evaluate side-chains 57 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.391 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0372 time to fit residues: 0.6079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 0.2980 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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: 0.7792 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 3472 Z= 0.221 Angle : 0.652 9.500 4720 Z= 0.321 Chirality : 0.043 0.232 515 Planarity : 0.003 0.031 605 Dihedral : 4.388 22.917 474 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.26 % Favored : 90.50 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.69 (0.42), residues: 421 helix: -2.03 (1.22), residues: 20 sheet: 0.71 (0.58), residues: 93 loop : -1.80 (0.35), residues: 308 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.395 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 58 average time/residue: 0.1656 time to fit residues: 11.7774 Evaluate side-chains 57 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.397 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0345 time to fit residues: 0.5740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.120573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.094341 restraints weight = 8267.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.096747 restraints weight = 5611.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.098332 restraints weight = 4394.599| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 3472 Z= 0.292 Angle : 0.690 9.465 4720 Z= 0.343 Chirality : 0.044 0.230 515 Planarity : 0.004 0.031 605 Dihedral : 4.785 23.609 474 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.88 % Favored : 87.89 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.92 (0.41), residues: 421 helix: -2.79 (0.99), residues: 26 sheet: 0.49 (0.57), residues: 90 loop : -1.84 (0.35), residues: 305 =============================================================================== Job complete usr+sys time: 1241.11 seconds wall clock time: 22 minutes 48.45 seconds (1368.45 seconds total)