Starting phenix.real_space_refine on Mon Jun 24 15:24:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xe9_38283/06_2024/8xe9_38283.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xe9_38283/06_2024/8xe9_38283.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xe9_38283/06_2024/8xe9_38283.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xe9_38283/06_2024/8xe9_38283.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xe9_38283/06_2024/8xe9_38283.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xe9_38283/06_2024/8xe9_38283.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2079 2.51 5 N 554 2.21 5 O 618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 93": "OD1" <-> "OD2" Residue "C GLU 340": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 3266 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 888 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "B" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "C" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1557 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 13, 'TRANS': 182} Time building chain proxies: 2.58, per 1000 atoms: 0.79 Number of scatterers: 3266 At special positions: 0 Unit cell: (61.56, 76.95, 89.91, 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 618 8.00 N 554 7.00 C 2079 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " 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: 1.08 Conformation dependent library (CDL) restraints added in 882.4 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 768 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 10 sheets defined 6.2% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.681A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.724A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.556A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 removed outlier: 3.801A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 removed outlier: 6.771A pdb=" N MET A 34 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 48 " --> pdb=" O TRP A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 54 removed outlier: 6.453A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N TYR B 91 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N THR B 98 " --> pdb=" O TYR B 91 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP B 93 " --> pdb=" O LEU B 96 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 379 through 380 Processing sheet with id=AA8, first strand: chain 'C' and resid 400 through 402 removed outlier: 3.535A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'C' and resid 473 through 474 87 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: 0.81 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1046 1.34 - 1.46: 873 1.46 - 1.58: 1416 1.58 - 1.70: 0 1.70 - 1.82: 18 Bond restraints: 3353 Sorted by residual: bond pdb=" CB PRO C 445 " pdb=" CG PRO C 445 " ideal model delta sigma weight residual 1.492 1.559 -0.067 5.00e-02 4.00e+02 1.78e+00 bond pdb=" CA GLY B 68 " pdb=" C GLY B 68 " ideal model delta sigma weight residual 1.514 1.530 -0.016 1.41e-02 5.03e+03 1.23e+00 bond pdb=" C ILE C 418 " pdb=" O ILE C 418 " ideal model delta sigma weight residual 1.231 1.242 -0.011 1.02e-02 9.61e+03 1.06e+00 bond pdb=" N GLY B 68 " pdb=" CA GLY B 68 " ideal model delta sigma weight residual 1.449 1.464 -0.015 1.45e-02 4.76e+03 1.06e+00 bond pdb=" CG PRO B 95 " pdb=" CD PRO B 95 " ideal model delta sigma weight residual 1.512 1.486 0.026 2.70e-02 1.37e+03 9.21e-01 ... (remaining 3348 not shown) Histogram of bond angle deviations from ideal: 100.37 - 107.09: 111 107.09 - 113.81: 1755 113.81 - 120.53: 1260 120.53 - 127.25: 1394 127.25 - 133.97: 40 Bond angle restraints: 4560 Sorted by residual: angle pdb=" C SER C 486 " pdb=" CA SER C 486 " pdb=" CB SER C 486 " ideal model delta sigma weight residual 110.42 115.91 -5.49 1.99e+00 2.53e-01 7.60e+00 angle pdb=" N VAL C 524 " pdb=" CA VAL C 524 " pdb=" C VAL C 524 " ideal model delta sigma weight residual 106.72 110.81 -4.09 1.59e+00 3.96e-01 6.62e+00 angle pdb=" CA PRO C 445 " pdb=" N PRO C 445 " pdb=" CD PRO C 445 " ideal model delta sigma weight residual 112.00 108.80 3.20 1.40e+00 5.10e-01 5.21e+00 angle pdb=" C VAL C 362 " pdb=" N ALA C 363 " pdb=" CA ALA C 363 " ideal model delta sigma weight residual 121.97 125.54 -3.57 1.73e+00 3.34e-01 4.25e+00 angle pdb=" C GLY B 50 " pdb=" N ALA B 51 " pdb=" CA ALA B 51 " ideal model delta sigma weight residual 121.54 125.36 -3.82 1.91e+00 2.74e-01 4.00e+00 ... (remaining 4555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 1785 17.86 - 35.72: 161 35.72 - 53.58: 23 53.58 - 71.45: 5 71.45 - 89.31: 2 Dihedral angle restraints: 1976 sinusoidal: 765 harmonic: 1211 Sorted by residual: dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 95 " pdb=" CB CYS A 95 " ideal model delta sinusoidal sigma weight residual 93.00 153.06 -60.06 1 1.00e+01 1.00e-02 4.81e+01 dihedral pdb=" CA ARG A 97 " pdb=" C ARG A 97 " pdb=" N ASP A 98 " pdb=" CA ASP A 98 " ideal model delta harmonic sigma weight residual -180.00 -159.64 -20.36 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual -86.00 -52.42 -33.58 1 1.00e+01 1.00e-02 1.60e+01 ... (remaining 1973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 261 0.027 - 0.054: 143 0.054 - 0.081: 47 0.081 - 0.108: 23 0.108 - 0.134: 13 Chirality restraints: 487 Sorted by residual: chirality pdb=" CA VAL C 401 " pdb=" N VAL C 401 " pdb=" C VAL C 401 " pdb=" CB VAL C 401 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA ILE B 48 " pdb=" N ILE B 48 " pdb=" C ILE B 48 " pdb=" CB ILE B 48 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ILE C 468 " pdb=" N ILE C 468 " pdb=" C ILE C 468 " pdb=" CB ILE C 468 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.58e-01 ... (remaining 484 not shown) Planarity restraints: 591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 444 " 0.065 5.00e-02 4.00e+02 9.75e-02 1.52e+01 pdb=" N PRO C 445 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO C 445 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 445 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 94 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO B 95 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 95 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 95 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 462 " 0.021 5.00e-02 4.00e+02 3.20e-02 1.64e+00 pdb=" N PRO C 463 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO C 463 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 463 " 0.018 5.00e-02 4.00e+02 ... (remaining 588 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 786 2.79 - 3.32: 2757 3.32 - 3.85: 5147 3.85 - 4.37: 6163 4.37 - 4.90: 11124 Nonbonded interactions: 25977 Sorted by model distance: nonbonded pdb=" OD2 ASP C 398 " pdb=" OH TYR C 423 " model vdw 2.265 2.440 nonbonded pdb=" NH2 ARG A 102 " pdb=" O SER C 490 " model vdw 2.311 2.520 nonbonded pdb=" NH2 ARG C 454 " pdb=" O SER C 469 " model vdw 2.316 2.520 nonbonded pdb=" NH1 ARG A 102 " pdb=" OE1 GLN C 493 " model vdw 2.351 2.520 nonbonded pdb=" OH TYR A 33 " pdb=" O LEU C 455 " model vdw 2.362 2.440 ... (remaining 25972 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 5.500 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.670 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 3353 Z= 0.167 Angle : 0.557 5.488 4560 Z= 0.299 Chirality : 0.042 0.134 487 Planarity : 0.005 0.097 591 Dihedral : 13.283 89.308 1190 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.41), residues: 414 helix: -4.97 (0.25), residues: 27 sheet: -1.46 (0.53), residues: 116 loop : -0.94 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 436 HIS 0.001 0.000 HIS C 339 PHE 0.010 0.001 PHE C 456 TYR 0.009 0.001 TYR B 91 ARG 0.004 0.000 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 35 THR cc_start: 0.8623 (m) cc_final: 0.8423 (t) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1946 time to fit residues: 20.5659 Evaluate side-chains 58 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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: 3.9990 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 39 GLN B 38 GLN B 89 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3353 Z= 0.232 Angle : 0.628 6.963 4560 Z= 0.329 Chirality : 0.043 0.191 487 Planarity : 0.005 0.064 591 Dihedral : 4.405 21.754 464 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 2.55 % Allowed : 13.60 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.41), residues: 414 helix: -4.91 (0.24), residues: 26 sheet: -0.89 (0.51), residues: 118 loop : -1.04 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 35 HIS 0.002 0.001 HIS C 519 PHE 0.008 0.001 PHE A 27 TYR 0.013 0.001 TYR B 91 ARG 0.003 0.001 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 GLU cc_start: 0.7143 (mp0) cc_final: 0.6840 (mp0) REVERT: A 104 GLU cc_start: 0.7128 (tm-30) cc_final: 0.6866 (tm-30) REVERT: B 5 THR cc_start: 0.8698 (m) cc_final: 0.8426 (p) outliers start: 9 outliers final: 6 residues processed: 70 average time/residue: 0.1478 time to fit residues: 12.7637 Evaluate side-chains 66 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 107 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 0.0370 chunk 27 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN B 38 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3353 Z= 0.174 Angle : 0.565 5.396 4560 Z= 0.297 Chirality : 0.042 0.138 487 Planarity : 0.005 0.053 591 Dihedral : 4.153 20.880 464 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.68 % Allowed : 14.16 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.41), residues: 414 helix: -4.89 (0.30), residues: 20 sheet: -0.60 (0.50), residues: 124 loop : -0.86 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 36 HIS 0.001 0.000 HIS C 519 PHE 0.010 0.001 PHE C 392 TYR 0.010 0.001 TYR B 91 ARG 0.003 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 0.346 Fit side-chains REVERT: B 70 GLU cc_start: 0.7324 (mm-30) cc_final: 0.7089 (mm-30) outliers start: 13 outliers final: 10 residues processed: 71 average time/residue: 0.1402 time to fit residues: 12.4757 Evaluate side-chains 70 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 456 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 0.1980 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 0.0670 chunk 10 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 overall best weight: 2.0524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 3353 Z= 0.370 Angle : 0.639 6.043 4560 Z= 0.338 Chirality : 0.044 0.141 487 Planarity : 0.005 0.045 591 Dihedral : 4.486 24.244 464 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.39 % Favored : 89.61 % Rotamer: Outliers : 4.82 % Allowed : 16.43 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.41), residues: 414 helix: -4.93 (0.22), residues: 26 sheet: -0.49 (0.50), residues: 130 loop : -1.05 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.001 0.000 HIS C 519 PHE 0.009 0.001 PHE C 392 TYR 0.022 0.002 TYR B 91 ARG 0.007 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 59 time to evaluate : 0.314 Fit side-chains REVERT: B 30 ASN cc_start: 0.8261 (p0) cc_final: 0.8026 (p0) REVERT: C 436 TRP cc_start: 0.7286 (OUTLIER) cc_final: 0.6700 (m-10) outliers start: 17 outliers final: 14 residues processed: 66 average time/residue: 0.1302 time to fit residues: 10.8297 Evaluate side-chains 72 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 57 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 511 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 0.2980 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 38 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3353 Z= 0.358 Angle : 0.638 6.594 4560 Z= 0.337 Chirality : 0.044 0.144 487 Planarity : 0.005 0.041 591 Dihedral : 4.550 24.629 464 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 5.67 % Allowed : 17.56 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.41), residues: 414 helix: -4.88 (0.22), residues: 26 sheet: -0.48 (0.49), residues: 130 loop : -1.07 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.001 0.000 HIS C 519 PHE 0.010 0.001 PHE C 392 TYR 0.017 0.002 TYR B 91 ARG 0.005 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 55 time to evaluate : 0.409 Fit side-chains REVERT: B 30 ASN cc_start: 0.8273 (p0) cc_final: 0.8011 (p0) REVERT: C 436 TRP cc_start: 0.7283 (OUTLIER) cc_final: 0.6602 (m-10) outliers start: 20 outliers final: 15 residues processed: 64 average time/residue: 0.1576 time to fit residues: 12.4781 Evaluate side-chains 69 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 53 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 511 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3353 Z= 0.218 Angle : 0.618 6.600 4560 Z= 0.326 Chirality : 0.043 0.146 487 Planarity : 0.005 0.052 591 Dihedral : 4.449 23.309 464 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 5.10 % Allowed : 20.40 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.41), residues: 414 helix: -4.74 (0.28), residues: 26 sheet: -0.28 (0.50), residues: 124 loop : -1.01 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 36 HIS 0.000 0.000 HIS C 339 PHE 0.008 0.001 PHE C 392 TYR 0.013 0.001 TYR B 36 ARG 0.011 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 60 time to evaluate : 0.373 Fit side-chains REVERT: B 30 ASN cc_start: 0.8201 (p0) cc_final: 0.7945 (p0) outliers start: 18 outliers final: 14 residues processed: 69 average time/residue: 0.1486 time to fit residues: 12.7127 Evaluate side-chains 70 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 56 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TRP Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 511 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 38 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.5423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3353 Z= 0.327 Angle : 0.658 7.271 4560 Z= 0.346 Chirality : 0.045 0.145 487 Planarity : 0.005 0.060 591 Dihedral : 4.617 24.182 464 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 5.10 % Allowed : 18.41 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.41), residues: 414 helix: -4.56 (0.40), residues: 26 sheet: -0.32 (0.49), residues: 130 loop : -1.06 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.001 0.000 HIS C 339 PHE 0.009 0.001 PHE C 392 TYR 0.012 0.001 TYR B 36 ARG 0.012 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 56 time to evaluate : 0.403 Fit side-chains REVERT: B 30 ASN cc_start: 0.8281 (p0) cc_final: 0.8002 (p0) REVERT: C 436 TRP cc_start: 0.7264 (OUTLIER) cc_final: 0.6548 (m-10) outliers start: 18 outliers final: 15 residues processed: 65 average time/residue: 0.1661 time to fit residues: 13.3326 Evaluate side-chains 72 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 56 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TRP Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 511 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN B 6 GLN B 38 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.5474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3353 Z= 0.217 Angle : 0.648 6.934 4560 Z= 0.342 Chirality : 0.044 0.146 487 Planarity : 0.005 0.058 591 Dihedral : 4.498 23.217 464 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 4.53 % Allowed : 20.11 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.42), residues: 414 helix: -4.40 (0.51), residues: 26 sheet: -0.16 (0.48), residues: 135 loop : -1.04 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.000 0.000 HIS C 519 PHE 0.008 0.001 PHE C 392 TYR 0.010 0.001 TYR C 396 ARG 0.013 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 57 time to evaluate : 0.387 Fit side-chains REVERT: B 30 ASN cc_start: 0.8222 (p0) cc_final: 0.7971 (p0) outliers start: 16 outliers final: 12 residues processed: 65 average time/residue: 0.1574 time to fit residues: 12.7904 Evaluate side-chains 68 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 56 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TRP Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 456 PHE 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: 0.7980 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.5638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3353 Z= 0.223 Angle : 0.643 6.927 4560 Z= 0.339 Chirality : 0.043 0.150 487 Planarity : 0.005 0.062 591 Dihedral : 4.366 21.465 464 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 4.53 % Allowed : 20.96 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.41), residues: 414 helix: -4.26 (0.59), residues: 26 sheet: -0.26 (0.48), residues: 134 loop : -1.09 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 36 HIS 0.000 0.000 HIS C 505 PHE 0.011 0.001 PHE C 400 TYR 0.011 0.001 TYR C 396 ARG 0.014 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 61 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: B 30 ASN cc_start: 0.8183 (p0) cc_final: 0.7907 (p0) outliers start: 16 outliers final: 11 residues processed: 69 average time/residue: 0.1666 time to fit residues: 14.0372 Evaluate side-chains 69 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TRP Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 456 PHE 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: 5.9990 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.5734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3353 Z= 0.213 Angle : 0.656 6.717 4560 Z= 0.343 Chirality : 0.043 0.150 487 Planarity : 0.004 0.038 591 Dihedral : 4.304 20.673 464 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 3.12 % Allowed : 22.38 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.41), residues: 414 helix: -4.21 (0.63), residues: 26 sheet: -0.23 (0.48), residues: 128 loop : -1.04 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.000 0.000 HIS C 339 PHE 0.011 0.001 PHE C 400 TYR 0.012 0.001 TYR C 396 ARG 0.003 0.000 ARG B 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: B 30 ASN cc_start: 0.8179 (p0) cc_final: 0.7908 (p0) outliers start: 11 outliers final: 11 residues processed: 61 average time/residue: 0.1753 time to fit residues: 12.9044 Evaluate side-chains 68 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TRP Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 456 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 21 optimal weight: 0.0470 chunk 27 optimal weight: 0.6980 chunk 1 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** 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 = 0.3090 r_free = 0.3090 target = 0.064398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.051784 restraints weight = 9926.746| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 3.96 r_work: 0.2699 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.5834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3353 Z= 0.179 Angle : 0.634 6.198 4560 Z= 0.333 Chirality : 0.042 0.136 487 Planarity : 0.004 0.037 591 Dihedral : 4.112 18.609 464 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 2.83 % Allowed : 22.38 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.41), residues: 414 helix: -4.14 (0.65), residues: 26 sheet: -0.13 (0.52), residues: 111 loop : -0.89 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 36 HIS 0.000 0.000 HIS C 519 PHE 0.013 0.001 PHE C 400 TYR 0.013 0.001 TYR C 396 ARG 0.003 0.000 ARG C 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1241.35 seconds wall clock time: 22 minutes 56.75 seconds (1376.75 seconds total)