Starting phenix.real_space_refine (version: dev) on Fri Feb 17 04:15:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtg_32785/02_2023/7wtg_32785.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtg_32785/02_2023/7wtg_32785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtg_32785/02_2023/7wtg_32785.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtg_32785/02_2023/7wtg_32785.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtg_32785/02_2023/7wtg_32785.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtg_32785/02_2023/7wtg_32785.pdb" } resolution = 3.8 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= 0.001 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 "E PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 420": "OD1" <-> "OD2" Residue "E ASP 442": "OD1" <-> "OD2" Residue "E GLU 465": "OE1" <-> "OE2" Residue "E TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 86": "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: 3318 Number of models: 1 Model: "" Number of chains: 3 Chain: "E" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "H" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 788 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Time building chain proxies: 2.31, per 1000 atoms: 0.70 Number of scatterers: 3318 At special positions: 0 Unit cell: (60.32, 64.48, 115.44, 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 17 16.00 O 631 8.00 N 563 7.00 C 2107 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.02 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.05 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 503.1 milliseconds 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 778 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 8 sheets defined 5.2% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'E' and resid 337 through 343 removed outlier: 3.596A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 403 through 405 No H-bonds generated for 'chain 'E' and resid 403 through 405' Processing helix chain 'E' and resid 406 through 411 removed outlier: 3.762A pdb=" N ILE E 410 " --> pdb=" O GLU E 406 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA E 411 " --> pdb=" O VAL E 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 406 through 411' Processing sheet with id=AA1, first strand: chain 'E' and resid 356 through 358 removed outlier: 4.408A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.513A pdb=" N ASN H 59 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ALA H 33 " --> pdb=" O LEU H 99 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU H 99 " --> pdb=" O ALA H 33 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AA7, first strand: chain 'L' and resid 45 through 48 removed outlier: 7.248A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 45 through 48 removed outlier: 7.248A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 74 hydrogen bonds defined for protein. 180 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: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1064 1.35 - 1.47: 930 1.47 - 1.60: 1389 1.60 - 1.73: 0 1.73 - 1.85: 21 Bond restraints: 3404 Sorted by residual: bond pdb=" N VAL E 445 " pdb=" CA VAL E 445 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.77e+00 bond pdb=" N LYS E 444 " pdb=" CA LYS E 444 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.21e-02 6.83e+03 7.14e+00 bond pdb=" N GLY E 447 " pdb=" CA GLY E 447 " ideal model delta sigma weight residual 1.450 1.476 -0.025 1.01e-02 9.80e+03 6.18e+00 bond pdb=" N SER E 446 " pdb=" CA SER E 446 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.21e-02 6.83e+03 4.66e+00 bond pdb=" CA VAL L 58 " pdb=" CB VAL L 58 " ideal model delta sigma weight residual 1.537 1.563 -0.026 1.29e-02 6.01e+03 4.06e+00 ... (remaining 3399 not shown) Histogram of bond angle deviations from ideal: 97.47 - 104.80: 62 104.80 - 112.14: 1497 112.14 - 119.47: 1237 119.47 - 126.81: 1775 126.81 - 134.15: 49 Bond angle restraints: 4620 Sorted by residual: angle pdb=" C ILE E 410 " pdb=" N ALA E 411 " pdb=" CA ALA E 411 " ideal model delta sigma weight residual 120.60 127.40 -6.80 1.53e+00 4.27e-01 1.98e+01 angle pdb=" C GLY H 113 " pdb=" N MET H 114 " pdb=" CA MET H 114 " ideal model delta sigma weight residual 121.54 129.65 -8.11 1.91e+00 2.74e-01 1.80e+01 angle pdb=" N TYR L 94 " pdb=" CA TYR L 94 " pdb=" C TYR L 94 " ideal model delta sigma weight residual 109.81 119.12 -9.31 2.21e+00 2.05e-01 1.77e+01 angle pdb=" CA GLY E 447 " pdb=" C GLY E 447 " pdb=" O GLY E 447 " ideal model delta sigma weight residual 122.05 118.00 4.05 1.00e+00 1.00e+00 1.64e+01 angle pdb=" C GLN H 62 " pdb=" N LYS H 63 " pdb=" CA LYS H 63 " ideal model delta sigma weight residual 121.54 128.80 -7.26 1.91e+00 2.74e-01 1.44e+01 ... (remaining 4615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 1798 17.95 - 35.90: 181 35.90 - 53.84: 29 53.84 - 71.79: 4 71.79 - 89.74: 5 Dihedral angle restraints: 2017 sinusoidal: 790 harmonic: 1227 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 165.13 -72.13 1 1.00e+01 1.00e-02 6.65e+01 dihedral pdb=" CA CYS E 361 " pdb=" C CYS E 361 " pdb=" N VAL E 362 " pdb=" CA VAL E 362 " ideal model delta harmonic sigma weight residual 180.00 141.00 39.00 0 5.00e+00 4.00e-02 6.08e+01 dihedral pdb=" CA PRO E 337 " pdb=" C PRO E 337 " pdb=" N PHE E 338 " pdb=" CA PHE E 338 " ideal model delta harmonic sigma weight residual 180.00 149.52 30.48 0 5.00e+00 4.00e-02 3.72e+01 ... (remaining 2014 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 349 0.058 - 0.116: 95 0.116 - 0.174: 34 0.174 - 0.233: 8 0.233 - 0.291: 4 Chirality restraints: 490 Sorted by residual: chirality pdb=" CB THR L 85 " pdb=" CA THR L 85 " pdb=" OG1 THR L 85 " pdb=" CG2 THR L 85 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CB VAL L 58 " pdb=" CA VAL L 58 " pdb=" CG1 VAL L 58 " pdb=" CG2 VAL L 58 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA ASN E 354 " pdb=" N ASN E 354 " pdb=" C ASN E 354 " pdb=" CB ASN E 354 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 487 not shown) Planarity restraints: 601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS E 462 " 0.053 5.00e-02 4.00e+02 8.00e-02 1.02e+01 pdb=" N PRO E 463 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO E 463 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO E 463 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 453 " 0.022 2.00e-02 2.50e+03 2.12e-02 9.01e+00 pdb=" CG TYR E 453 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR E 453 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR E 453 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR E 453 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR E 453 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR E 453 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR E 453 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL L 58 " 0.049 5.00e-02 4.00e+02 7.48e-02 8.96e+00 pdb=" N PRO L 59 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO L 59 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO L 59 " 0.041 5.00e-02 4.00e+02 ... (remaining 598 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 922 2.82 - 3.34: 2655 3.34 - 3.86: 5232 3.86 - 4.38: 5684 4.38 - 4.90: 10127 Nonbonded interactions: 24620 Sorted by model distance: nonbonded pdb=" O SER L 60 " pdb=" OG SER L 60 " model vdw 2.297 2.440 nonbonded pdb=" O ILE L 2 " pdb=" OG1 THR L 97 " model vdw 2.349 2.440 nonbonded pdb=" NH2 ARG H 67 " pdb=" OD2 ASP H 90 " model vdw 2.364 2.520 nonbonded pdb=" OD2 ASP E 398 " pdb=" OH TYR E 423 " model vdw 2.396 2.440 nonbonded pdb=" OG1 THR L 85 " pdb=" O GLY L 101 " model vdw 2.398 2.440 ... (remaining 24615 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 17 5.16 5 C 2107 2.51 5 N 563 2.21 5 O 631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.400 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: 10.020 Check model and map are aligned: 0.040 Process input model: 13.200 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.050 3404 Z= 0.390 Angle : 1.201 11.712 4620 Z= 0.644 Chirality : 0.069 0.291 490 Planarity : 0.011 0.083 601 Dihedral : 14.445 89.737 1221 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -2.94 (0.36), residues: 419 helix: -4.41 (0.43), residues: 30 sheet: -0.69 (0.47), residues: 125 loop : -2.41 (0.32), residues: 264 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1879 time to fit residues: 19.8537 Evaluate side-chains 76 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.375 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5205 ------------------------------------------------------------------------------- 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: 0.9980 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.0980 chunk 10 optimal weight: 0.2980 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 0.0270 chunk 12 optimal weight: 0.7980 chunk 20 optimal weight: 0.1980 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.2438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN L 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 3404 Z= 0.203 Angle : 0.631 7.132 4620 Z= 0.327 Chirality : 0.045 0.179 490 Planarity : 0.006 0.062 601 Dihedral : 5.695 33.095 470 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.37), residues: 419 helix: -3.79 (0.62), residues: 30 sheet: -0.44 (0.48), residues: 120 loop : -2.28 (0.33), residues: 269 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 83 average time/residue: 0.1945 time to fit residues: 19.0243 Evaluate side-chains 85 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 0.387 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0408 time to fit residues: 0.9529 ------------------------------------------------------------------------------- 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: 1.9990 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 0.0010 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 chunk 30 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 360 ASN L 55 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 3404 Z= 0.251 Angle : 0.633 7.722 4620 Z= 0.327 Chirality : 0.046 0.194 490 Planarity : 0.005 0.052 601 Dihedral : 5.612 33.422 470 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.26 (0.38), residues: 419 helix: -2.69 (0.99), residues: 24 sheet: -0.41 (0.48), residues: 119 loop : -2.01 (0.34), residues: 276 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 87 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 88 average time/residue: 0.2062 time to fit residues: 21.1605 Evaluate side-chains 74 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 71 time to evaluate : 0.380 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0347 time to fit residues: 0.7134 ------------------------------------------------------------------------------- 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: 0.9980 chunk 18 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 0.0980 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 10 optimal weight: 0.0970 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 0.8980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 55 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 3404 Z= 0.311 Angle : 0.672 8.123 4620 Z= 0.346 Chirality : 0.047 0.216 490 Planarity : 0.006 0.050 601 Dihedral : 5.773 34.925 470 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer Outliers : 2.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.28 (0.38), residues: 419 helix: -2.31 (1.07), residues: 24 sheet: -0.67 (0.49), residues: 118 loop : -1.92 (0.33), residues: 277 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 79 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 83 average time/residue: 0.2170 time to fit residues: 20.9475 Evaluate side-chains 81 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 0.454 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0322 time to fit residues: 0.8561 ------------------------------------------------------------------------------- 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: 0.9980 chunk 34 optimal weight: 0.4980 chunk 28 optimal weight: 0.0770 chunk 0 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 0.0980 chunk 10 optimal weight: 0.0980 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 overall best weight: 0.2738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 343 ASN L 55 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 3404 Z= 0.210 Angle : 0.617 7.450 4620 Z= 0.316 Chirality : 0.044 0.179 490 Planarity : 0.005 0.051 601 Dihedral : 5.387 33.020 470 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer Outliers : 3.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.00 (0.39), residues: 419 helix: -2.01 (1.15), residues: 24 sheet: -0.43 (0.50), residues: 118 loop : -1.77 (0.34), residues: 277 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 81 average time/residue: 0.2008 time to fit residues: 18.9649 Evaluate side-chains 78 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.397 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0374 time to fit residues: 1.0119 ------------------------------------------------------------------------------- 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: 0.3980 chunk 40 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 13 optimal weight: 0.2980 chunk 21 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 343 ASN E 360 ASN E 477 ASN L 55 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 3404 Z= 0.310 Angle : 0.675 8.500 4620 Z= 0.349 Chirality : 0.047 0.220 490 Planarity : 0.005 0.050 601 Dihedral : 5.740 34.889 470 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer Outliers : 3.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.24 (0.38), residues: 419 helix: -2.64 (1.19), residues: 18 sheet: -0.67 (0.49), residues: 119 loop : -1.88 (0.33), residues: 282 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 2 residues processed: 85 average time/residue: 0.2076 time to fit residues: 20.6547 Evaluate side-chains 75 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 73 time to evaluate : 0.370 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0353 time to fit residues: 0.6781 ------------------------------------------------------------------------------- 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: 3.9990 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 0.3980 chunk 16 optimal weight: 0.5980 chunk 12 optimal weight: 0.3980 chunk 7 optimal weight: 0.0270 chunk 27 optimal weight: 0.1980 chunk 20 optimal weight: 0.8980 overall best weight: 0.3238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 360 ASN L 55 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 3404 Z= 0.231 Angle : 0.635 8.022 4620 Z= 0.326 Chirality : 0.045 0.195 490 Planarity : 0.005 0.052 601 Dihedral : 5.560 35.056 470 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.14 (0.39), residues: 419 helix: -2.45 (1.27), residues: 18 sheet: -0.55 (0.50), residues: 118 loop : -1.85 (0.34), residues: 283 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 80 average time/residue: 0.2382 time to fit residues: 22.6994 Evaluate side-chains 72 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 0.393 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0392 time to fit residues: 0.6569 ------------------------------------------------------------------------------- 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: 1.9990 chunk 31 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 360 ASN L 55 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.061 3404 Z= 0.492 Angle : 0.808 9.970 4620 Z= 0.423 Chirality : 0.052 0.288 490 Planarity : 0.006 0.052 601 Dihedral : 6.543 40.914 470 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.17 % Favored : 87.59 % Rotamer Outliers : 2.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.80 (0.37), residues: 419 helix: -3.08 (1.11), residues: 18 sheet: -1.05 (0.49), residues: 118 loop : -2.28 (0.32), residues: 283 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 86 average time/residue: 0.2041 time to fit residues: 20.5917 Evaluate side-chains 76 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 0.357 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0433 time to fit residues: 0.6804 ------------------------------------------------------------------------------- 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: 0.4980 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 18 optimal weight: 0.1980 chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 0.4980 chunk 25 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 360 ASN H 111 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 3404 Z= 0.336 Angle : 0.773 10.726 4620 Z= 0.400 Chirality : 0.050 0.244 490 Planarity : 0.006 0.054 601 Dihedral : 6.299 40.793 470 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.98 % Favored : 88.78 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: 419 helix: -3.58 (0.82), residues: 24 sheet: -0.91 (0.50), residues: 118 loop : -2.33 (0.32), residues: 277 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 82 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 84 average time/residue: 0.2150 time to fit residues: 20.8570 Evaluate side-chains 77 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 0.376 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0311 time to fit residues: 0.5558 ------------------------------------------------------------------------------- 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: 3.9990 chunk 26 optimal weight: 0.4980 chunk 35 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 chunk 30 optimal weight: 0.3980 chunk 4 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 3404 Z= 0.328 Angle : 0.781 9.960 4620 Z= 0.400 Chirality : 0.049 0.233 490 Planarity : 0.007 0.066 601 Dihedral : 6.223 40.389 470 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.74 % Favored : 89.02 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.38), residues: 419 helix: -3.03 (1.13), residues: 18 sheet: -0.88 (0.50), residues: 118 loop : -2.28 (0.32), residues: 283 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 79 average time/residue: 0.2130 time to fit residues: 19.6689 Evaluate side-chains 80 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 0.434 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0381 time to fit residues: 0.6935 ------------------------------------------------------------------------------- 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: 0.1980 chunk 1 optimal weight: 0.1980 chunk 24 optimal weight: 0.0980 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 0.2980 chunk 15 optimal weight: 0.0970 chunk 41 optimal weight: 0.9980 overall best weight: 0.1778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN L 55 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.166596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.141357 restraints weight = 4252.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.141805 restraints weight = 3829.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.142964 restraints weight = 3570.526| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 3404 Z= 0.202 Angle : 0.694 8.435 4620 Z= 0.352 Chirality : 0.046 0.162 490 Planarity : 0.006 0.055 601 Dihedral : 5.624 35.071 470 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.31 % Favored : 90.45 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.41 (0.39), residues: 419 helix: -2.65 (1.25), residues: 18 sheet: -0.65 (0.51), residues: 118 loop : -2.08 (0.33), residues: 283 =============================================================================== Job complete usr+sys time: 1384.64 seconds wall clock time: 25 minutes 50.15 seconds (1550.15 seconds total)