Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:17:44 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrl_32732/11_2022/7wrl_32732.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrl_32732/11_2022/7wrl_32732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrl_32732/11_2022/7wrl_32732.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrl_32732/11_2022/7wrl_32732.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrl_32732/11_2022/7wrl_32732.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrl_32732/11_2022/7wrl_32732.pdb" } resolution = 3.51 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= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 50": "NH1" <-> "NH2" Residue "A ARG 84": "NH1" <-> "NH2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 79": "NH1" <-> "NH2" Residue "B ASP 84": "OD1" <-> "OD2" Residue "R ARG 357": "NH1" <-> "NH2" Residue "R ASP 364": "OD1" <-> "OD2" Residue "R TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 457": "NH1" <-> "NH2" Residue "R GLU 471": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 3251 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 971 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "B" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 776 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "R" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1504 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain breaks: 1 Time building chain proxies: 2.44, per 1000 atoms: 0.75 Number of scatterers: 3251 At special positions: 0 Unit cell: (63.72, 82.08, 76.68, 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 636 8.00 N 548 7.00 C 2052 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.03 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.03 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: 1.20 Conformation dependent library (CDL) restraints added in 497.9 milliseconds 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 764 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 11 sheets defined 5.0% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 62 through 65 removed outlier: 3.969A pdb=" N GLN A 65 " --> pdb=" O ASP A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.608A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 384 through 390 removed outlier: 3.578A pdb=" N LEU R 387 " --> pdb=" O PRO R 384 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASN R 388 " --> pdb=" O THR R 385 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP R 389 " --> pdb=" O LYS R 386 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU R 390 " --> pdb=" O LEU R 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 384 through 390' Processing helix chain 'R' and resid 498 through 502 removed outlier: 3.785A pdb=" N TYR R 501 " --> pdb=" O ARG R 498 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLY R 502 " --> pdb=" O PRO R 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 498 through 502' Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 19 Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 39 removed outlier: 6.876A pdb=" N SER A 34 " --> pdb=" O ARG A 50 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ARG A 50 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 72 through 73 removed outlier: 3.508A pdb=" N ASP A 73 " --> pdb=" O THR A 78 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR A 78 " --> pdb=" O ASP A 73 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA6, first strand: chain 'A' and resid 97 through 101 removed outlier: 4.703A pdb=" N VAL A 119 " --> pdb=" O ARG A 98 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL A 100 " --> pdb=" O MET A 117 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N MET A 117 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 22 removed outlier: 3.831A pdb=" N SER B 65 " --> pdb=" O THR B 76 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 46 through 50 removed outlier: 6.537A pdb=" N TRP B 37 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 356 through 358 Processing sheet with id=AB1, first strand: chain 'R' and resid 361 through 362 removed outlier: 6.995A pdb=" N CYS R 361 " --> pdb=" O CYS R 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'R' and resid 452 through 454 51 hydrogen bonds defined for protein. 117 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.76 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1017 1.34 - 1.46: 739 1.46 - 1.57: 1558 1.57 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 3332 Sorted by residual: bond pdb=" C ASP A 109 " pdb=" N PHE A 110 " ideal model delta sigma weight residual 1.334 1.305 0.030 1.49e-02 4.50e+03 3.93e+00 bond pdb=" CB CYS B 90 " pdb=" SG CYS B 90 " ideal model delta sigma weight residual 1.808 1.757 0.051 3.30e-02 9.18e+02 2.39e+00 bond pdb=" C LYS A 13 " pdb=" N PRO A 14 " ideal model delta sigma weight residual 1.330 1.349 -0.019 1.25e-02 6.40e+03 2.35e+00 bond pdb=" N ALA R 411 " pdb=" CA ALA R 411 " ideal model delta sigma weight residual 1.457 1.436 0.021 1.41e-02 5.03e+03 2.13e+00 bond pdb=" C ALA R 372 " pdb=" N PRO R 373 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 2.04e+00 ... (remaining 3327 not shown) Histogram of bond angle deviations from ideal: 99.84 - 106.67: 88 106.67 - 113.50: 1690 113.50 - 120.33: 1256 120.33 - 127.16: 1467 127.16 - 133.99: 28 Bond angle restraints: 4529 Sorted by residual: angle pdb=" N VAL R 483 " pdb=" CA VAL R 483 " pdb=" C VAL R 483 " ideal model delta sigma weight residual 106.21 110.82 -4.61 1.07e+00 8.73e-01 1.86e+01 angle pdb=" C GLY R 485 " pdb=" N PHE R 486 " pdb=" CA PHE R 486 " ideal model delta sigma weight residual 121.54 129.41 -7.87 1.91e+00 2.74e-01 1.70e+01 angle pdb=" N VAL R 367 " pdb=" CA VAL R 367 " pdb=" C VAL R 367 " ideal model delta sigma weight residual 112.29 108.61 3.68 9.40e-01 1.13e+00 1.53e+01 angle pdb=" OG1 THR B 94 " pdb=" CB THR B 94 " pdb=" CG2 THR B 94 " ideal model delta sigma weight residual 109.30 102.03 7.27 2.00e+00 2.50e-01 1.32e+01 angle pdb=" C TYR B 51 " pdb=" N ASP B 52 " pdb=" CA ASP B 52 " ideal model delta sigma weight residual 121.71 116.85 4.86 1.39e+00 5.18e-01 1.22e+01 ... (remaining 4524 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 1709 17.40 - 34.79: 196 34.79 - 52.19: 33 52.19 - 69.59: 5 69.59 - 86.98: 1 Dihedral angle restraints: 1944 sinusoidal: 734 harmonic: 1210 Sorted by residual: dihedral pdb=" CA LYS A 13 " pdb=" C LYS A 13 " pdb=" N PRO A 14 " pdb=" CA PRO A 14 " ideal model delta harmonic sigma weight residual -180.00 -145.72 -34.28 0 5.00e+00 4.00e-02 4.70e+01 dihedral pdb=" CA TYR A 60 " pdb=" C TYR A 60 " pdb=" N ALA A 61 " pdb=" CA ALA A 61 " ideal model delta harmonic sigma weight residual 180.00 156.47 23.53 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA ARG R 466 " pdb=" C ARG R 466 " pdb=" N ASP R 467 " pdb=" CA ASP R 467 " ideal model delta harmonic sigma weight residual 180.00 158.19 21.81 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 1941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 307 0.047 - 0.094: 120 0.094 - 0.141: 43 0.141 - 0.188: 11 0.188 - 0.235: 4 Chirality restraints: 485 Sorted by residual: chirality pdb=" CB ILE A 51 " pdb=" CA ILE A 51 " pdb=" CG1 ILE A 51 " pdb=" CG2 ILE A 51 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA TYR B 51 " pdb=" N TYR B 51 " pdb=" C TYR B 51 " pdb=" CB TYR B 51 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB VAL R 483 " pdb=" CA VAL R 483 " pdb=" CG1 VAL R 483 " pdb=" CG2 VAL R 483 " both_signs ideal model delta sigma weight residual False -2.63 -2.85 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 482 not shown) Planarity restraints: 586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS R 462 " 0.050 5.00e-02 4.00e+02 7.53e-02 9.08e+00 pdb=" N PRO R 463 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO R 463 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO R 463 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 338 " -0.014 2.00e-02 2.50e+03 1.75e-02 5.37e+00 pdb=" CG PHE R 338 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE R 338 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE R 338 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE R 338 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE R 338 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE R 338 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 56 " 0.037 5.00e-02 4.00e+02 5.59e-02 5.00e+00 pdb=" N PRO B 57 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 57 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 57 " 0.031 5.00e-02 4.00e+02 ... (remaining 583 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 986 2.81 - 3.33: 2686 3.33 - 3.86: 5412 3.86 - 4.38: 6037 4.38 - 4.90: 10870 Nonbonded interactions: 25991 Sorted by model distance: nonbonded pdb=" OG1 THR R 415 " pdb=" OD2 ASP R 420 " model vdw 2.289 2.440 nonbonded pdb=" OH TYR B 32 " pdb=" OD2 ASP R 405 " model vdw 2.312 2.440 nonbonded pdb=" ND2 ASN B 54 " pdb=" O GLY B 66 " model vdw 2.322 2.520 nonbonded pdb=" O SER A 25 " pdb=" OG SER A 25 " model vdw 2.327 2.440 nonbonded pdb=" OD2 ASP R 398 " pdb=" OH TYR R 423 " model vdw 2.327 2.440 ... (remaining 25986 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2052 2.51 5 N 548 2.21 5 O 636 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: 1.680 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: 0.010 Extract box with map and model: 9.610 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.030 Process input model: 14.380 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 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 0.054 3332 Z= 0.401 Angle : 1.031 8.952 4529 Z= 0.594 Chirality : 0.060 0.235 485 Planarity : 0.008 0.075 586 Dihedral : 14.713 86.983 1171 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.38 % Favored : 86.62 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -4.19 (0.37), residues: 411 helix: -4.93 (0.34), residues: 27 sheet: -2.41 (0.46), residues: 118 loop : -2.86 (0.34), residues: 266 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.403 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1736 time to fit residues: 14.4031 Evaluate side-chains 50 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.418 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 5.9990 chunk 30 optimal weight: 0.0980 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 0.0010 chunk 19 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 36 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 3332 Z= 0.177 Angle : 0.579 5.802 4529 Z= 0.315 Chirality : 0.043 0.150 485 Planarity : 0.005 0.061 586 Dihedral : 6.123 24.282 466 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer Outliers : 1.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.88 (0.38), residues: 411 helix: -4.52 (0.56), residues: 27 sheet: -1.87 (0.47), residues: 119 loop : -2.85 (0.35), residues: 265 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 0.379 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 72 average time/residue: 0.1654 time to fit residues: 14.5131 Evaluate side-chains 65 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 0.409 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0376 time to fit residues: 0.7893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 10 optimal weight: 0.0060 chunk 36 optimal weight: 0.0000 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 overall best weight: 0.5602 ------------------------------------------------------------------------------- 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** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 3332 Z= 0.187 Angle : 0.573 7.665 4529 Z= 0.307 Chirality : 0.043 0.156 485 Planarity : 0.005 0.057 586 Dihedral : 5.635 24.222 466 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.92 % Favored : 88.08 % 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: -3.59 (0.38), residues: 411 helix: -4.41 (0.59), residues: 27 sheet: -1.36 (0.50), residues: 114 loop : -2.80 (0.34), residues: 270 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 0.429 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 67 average time/residue: 0.1542 time to fit residues: 12.7129 Evaluate side-chains 55 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.407 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0390 time to fit residues: 0.7323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 0.0030 chunk 38 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 10 optimal weight: 0.3980 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 3332 Z= 0.189 Angle : 0.554 5.831 4529 Z= 0.299 Chirality : 0.043 0.155 485 Planarity : 0.005 0.056 586 Dihedral : 5.391 20.443 466 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.68 % Favored : 88.32 % 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: -3.47 (0.39), residues: 411 helix: -4.41 (0.59), residues: 27 sheet: -1.12 (0.51), residues: 114 loop : -2.79 (0.35), residues: 270 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.356 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 58 average time/residue: 0.1712 time to fit residues: 12.0967 Evaluate side-chains 52 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 0.361 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0329 time to fit residues: 0.6119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 0.0070 chunk 22 optimal weight: 0.3980 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 3332 Z= 0.274 Angle : 0.599 6.829 4529 Z= 0.325 Chirality : 0.045 0.164 485 Planarity : 0.004 0.051 586 Dihedral : 5.578 21.368 466 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.92 % Favored : 88.08 % Rotamer Outliers : 2.54 % 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: -3.51 (0.39), residues: 411 helix: -4.43 (0.58), residues: 27 sheet: -1.33 (0.50), residues: 114 loop : -2.72 (0.35), residues: 270 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.389 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 60 average time/residue: 0.1622 time to fit residues: 12.0044 Evaluate side-chains 59 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 0.407 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0372 time to fit residues: 0.9195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.0000 chunk 32 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.0020 chunk 20 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.4192 ------------------------------------------------------------------------------- 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** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 3332 Z= 0.174 Angle : 0.553 6.856 4529 Z= 0.297 Chirality : 0.044 0.154 485 Planarity : 0.004 0.052 586 Dihedral : 5.116 16.761 466 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.46 % Favored : 89.54 % 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: -3.28 (0.40), residues: 411 helix: -4.32 (0.62), residues: 27 sheet: -1.09 (0.51), residues: 114 loop : -2.59 (0.36), residues: 270 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 65 time to evaluate : 0.417 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 66 average time/residue: 0.1607 time to fit residues: 12.9843 Evaluate side-chains 57 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.389 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0345 time to fit residues: 0.5810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 0.0670 chunk 26 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 3332 Z= 0.194 Angle : 0.559 7.080 4529 Z= 0.301 Chirality : 0.044 0.155 485 Planarity : 0.004 0.051 586 Dihedral : 5.066 16.818 466 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.44 % Favored : 88.56 % 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: -3.24 (0.39), residues: 411 helix: -4.33 (0.59), residues: 27 sheet: -1.00 (0.51), residues: 109 loop : -2.57 (0.36), residues: 275 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.404 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 60 average time/residue: 0.1586 time to fit residues: 11.7981 Evaluate side-chains 60 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.377 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0362 time to fit residues: 0.6301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 3332 Z= 0.219 Angle : 0.577 7.639 4529 Z= 0.312 Chirality : 0.045 0.156 485 Planarity : 0.004 0.050 586 Dihedral : 5.057 16.778 466 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.19 % Favored : 88.81 % 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: -3.30 (0.39), residues: 411 helix: -4.37 (0.61), residues: 27 sheet: -1.11 (0.50), residues: 109 loop : -2.58 (0.35), residues: 275 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.339 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 55 average time/residue: 0.1645 time to fit residues: 11.1384 Evaluate side-chains 54 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.314 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 25 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 3332 Z= 0.192 Angle : 0.563 7.660 4529 Z= 0.302 Chirality : 0.044 0.155 485 Planarity : 0.004 0.049 586 Dihedral : 4.999 20.069 466 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % 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: -3.39 (0.39), residues: 411 helix: -4.36 (0.61), residues: 27 sheet: -1.14 (0.48), residues: 119 loop : -2.72 (0.36), residues: 265 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 0.385 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 56 average time/residue: 0.1601 time to fit residues: 11.0760 Evaluate side-chains 54 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.405 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0343 time to fit residues: 0.6371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 chunk 27 optimal weight: 0.1980 chunk 1 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 3332 Z= 0.201 Angle : 0.579 8.110 4529 Z= 0.310 Chirality : 0.044 0.156 485 Planarity : 0.004 0.053 586 Dihedral : 4.972 19.170 466 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % 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: -3.32 (0.39), residues: 411 helix: -4.35 (0.61), residues: 27 sheet: -1.12 (0.50), residues: 109 loop : -2.61 (0.35), residues: 275 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 0.410 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 56 average time/residue: 0.1553 time to fit residues: 10.8393 Evaluate side-chains 52 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 0.398 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0591 time to fit residues: 0.6269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.140644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.112105 restraints weight = 5263.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.115454 restraints weight = 3339.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.117725 restraints weight = 2500.335| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 3332 Z= 0.228 Angle : 0.597 8.200 4529 Z= 0.319 Chirality : 0.044 0.157 485 Planarity : 0.004 0.053 586 Dihedral : 5.045 18.835 466 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.92 % Favored : 88.08 % 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: -3.33 (0.39), residues: 411 helix: -4.38 (0.59), residues: 27 sheet: -1.14 (0.50), residues: 109 loop : -2.60 (0.35), residues: 275 =============================================================================== Job complete usr+sys time: 1218.74 seconds wall clock time: 22 minutes 46.79 seconds (1366.79 seconds total)