Starting phenix.real_space_refine on Thu Dec 7 17:09:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e23_30950/12_2023/7e23_30950.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e23_30950/12_2023/7e23_30950.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/7e23_30950/12_2023/7e23_30950.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e23_30950/12_2023/7e23_30950.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e23_30950/12_2023/7e23_30950.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e23_30950/12_2023/7e23_30950.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= 0.053 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 13 5.16 5 C 2001 2.51 5 N 519 2.21 5 O 600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 357": "NH1" <-> "NH2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C GLU 79": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 3133 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "B" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 756 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 94} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.35, per 1000 atoms: 0.75 Number of scatterers: 3133 At special positions: 0 Unit cell: (60.48, 74.52, 99.36, 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 13 16.00 O 600 8.00 N 519 7.00 C 2001 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 343 " Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 593.6 milliseconds 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 736 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 8 sheets defined 4.7% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.628A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.614A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.574A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'B' and resid 19 through 22 Processing sheet with id=AA5, first strand: chain 'B' and resid 57 through 58 removed outlier: 3.541A pdb=" N ASN B 58 " --> pdb=" O GLU B 50 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU B 46 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N GLU B 50 " --> pdb=" O TRP B 34 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TRP B 34 " --> pdb=" O GLU B 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 91 through 92 removed outlier: 3.528A pdb=" N ALA B 91 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 19 through 23 removed outlier: 3.951A pdb=" N LEU C 73 " --> pdb=" O CYS C 23 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.593A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) 61 hydrogen bonds defined for protein. 141 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.70 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: 985 1.34 - 1.46: 836 1.46 - 1.58: 1379 1.58 - 1.70: 0 1.70 - 1.82: 14 Bond restraints: 3214 Sorted by residual: bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.12e+00 bond pdb=" CB ARG B 66 " pdb=" CG ARG B 66 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.64e+00 bond pdb=" C SER B 70 " pdb=" N VAL B 71 " ideal model delta sigma weight residual 1.334 1.316 0.017 1.24e-02 6.50e+03 1.92e+00 bond pdb=" C5 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.413 1.437 -0.024 2.00e-02 2.50e+03 1.39e+00 bond pdb=" CD ARG B 66 " pdb=" NE ARG B 66 " ideal model delta sigma weight residual 1.458 1.442 0.016 1.40e-02 5.10e+03 1.27e+00 ... (remaining 3209 not shown) Histogram of bond angle deviations from ideal: 101.11 - 107.68: 138 107.68 - 114.24: 1732 114.24 - 120.81: 1304 120.81 - 127.38: 1166 127.38 - 133.95: 37 Bond angle restraints: 4377 Sorted by residual: angle pdb=" N ARG C 61 " pdb=" CA ARG C 61 " pdb=" C ARG C 61 " ideal model delta sigma weight residual 114.75 108.44 6.31 1.26e+00 6.30e-01 2.51e+01 angle pdb=" CG ARG B 66 " pdb=" CD ARG B 66 " pdb=" NE ARG B 66 " ideal model delta sigma weight residual 112.00 101.99 10.01 2.20e+00 2.07e-01 2.07e+01 angle pdb=" C SER C 92 " pdb=" N ASN C 93 " pdb=" CA ASN C 93 " ideal model delta sigma weight residual 121.54 129.87 -8.33 1.91e+00 2.74e-01 1.90e+01 angle pdb=" C GLY C 68 " pdb=" N THR C 69 " pdb=" CA THR C 69 " ideal model delta sigma weight residual 121.54 128.28 -6.74 1.91e+00 2.74e-01 1.25e+01 angle pdb=" C ASN C 93 " pdb=" N TRP C 94 " pdb=" CA TRP C 94 " ideal model delta sigma weight residual 121.80 113.47 8.33 2.44e+00 1.68e-01 1.17e+01 ... (remaining 4372 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 1699 17.73 - 35.46: 159 35.46 - 53.19: 27 53.19 - 70.92: 5 70.92 - 88.64: 4 Dihedral angle restraints: 1894 sinusoidal: 733 harmonic: 1161 Sorted by residual: dihedral pdb=" CA PHE C 71 " pdb=" C PHE C 71 " pdb=" N THR C 72 " pdb=" CA THR C 72 " ideal model delta harmonic sigma weight residual 180.00 137.99 42.01 0 5.00e+00 4.00e-02 7.06e+01 dihedral pdb=" CA SER C 7 " pdb=" C SER C 7 " pdb=" N PRO C 8 " pdb=" CA PRO C 8 " ideal model delta harmonic sigma weight residual 180.00 -157.15 -22.85 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA THR C 69 " pdb=" C THR C 69 " pdb=" N ASP C 70 " pdb=" CA ASP C 70 " ideal model delta harmonic sigma weight residual 180.00 157.31 22.69 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 1891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 301 0.039 - 0.078: 124 0.078 - 0.117: 35 0.117 - 0.156: 16 0.156 - 0.195: 3 Chirality restraints: 479 Sorted by residual: chirality pdb=" CA PHE C 71 " pdb=" N PHE C 71 " pdb=" C PHE C 71 " pdb=" CB PHE C 71 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.46e-01 chirality pdb=" CB ILE C 58 " pdb=" CA ILE C 58 " pdb=" CG1 ILE C 58 " pdb=" CG2 ILE C 58 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.13e-01 chirality pdb=" CA ILE A 434 " pdb=" N ILE A 434 " pdb=" C ILE A 434 " pdb=" CB ILE A 434 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.73e-01 ... (remaining 476 not shown) Planarity restraints: 562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 60 " 0.039 5.00e-02 4.00e+02 5.88e-02 5.53e+00 pdb=" N PRO B 61 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 61 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 61 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 71 " -0.022 2.00e-02 2.50e+03 1.62e-02 4.61e+00 pdb=" CG PHE C 71 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE C 71 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE C 71 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 71 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 71 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 71 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 47 " 0.008 2.00e-02 2.50e+03 1.22e-02 3.74e+00 pdb=" CG TRP B 47 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP B 47 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP B 47 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 47 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 47 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 47 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 47 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 47 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 47 " 0.002 2.00e-02 2.50e+03 ... (remaining 559 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 82 2.68 - 3.23: 2966 3.23 - 3.79: 4598 3.79 - 4.34: 6234 4.34 - 4.90: 10604 Nonbonded interactions: 24484 Sorted by model distance: nonbonded pdb=" OH TYR C 36 " pdb=" OE1 GLN C 89 " model vdw 2.123 2.440 nonbonded pdb=" O SER C 63 " pdb=" OG SER C 77 " model vdw 2.215 2.440 nonbonded pdb=" OG SER C 7 " pdb=" OG SER C 22 " model vdw 2.220 2.440 nonbonded pdb=" O LYS A 417 " pdb=" ND2 ASN A 422 " model vdw 2.239 2.520 nonbonded pdb=" OG SER B 28 " pdb=" O HIS B 53 " model vdw 2.246 2.440 ... (remaining 24479 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: 1.460 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: 6.770 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.420 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: 24.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 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 : 0.004 0.049 3214 Z= 0.291 Angle : 0.825 10.007 4377 Z= 0.456 Chirality : 0.051 0.195 479 Planarity : 0.006 0.059 561 Dihedral : 14.521 88.644 1143 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.30 % Favored : 82.70 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -3.70 (0.41), residues: 393 helix: -5.03 (0.42), residues: 20 sheet: -2.14 (0.45), residues: 125 loop : -2.50 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 47 HIS 0.000 0.000 HIS A 519 PHE 0.036 0.002 PHE C 71 TYR 0.017 0.002 TYR C 49 ARG 0.004 0.001 ARG C 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.376 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1792 time to fit residues: 12.5369 Evaluate side-chains 46 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.334 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 3214 Z= 0.316 Angle : 0.765 8.903 4377 Z= 0.390 Chirality : 0.050 0.204 479 Planarity : 0.008 0.127 561 Dihedral : 7.191 43.357 463 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.81 % Favored : 82.19 % Rotamer: Outliers : 2.07 % Allowed : 11.24 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -3.48 (0.42), residues: 393 helix: -4.94 (0.49), residues: 18 sheet: -2.11 (0.46), residues: 121 loop : -2.30 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 436 HIS 0.000 0.000 HIS A 519 PHE 0.039 0.002 PHE C 71 TYR 0.014 0.002 TYR C 49 ARG 0.014 0.001 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.352 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 49 average time/residue: 0.1376 time to fit residues: 8.5584 Evaluate side-chains 46 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.352 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0347 time to fit residues: 0.7770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 0.0570 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 38 optimal weight: 0.2980 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3214 Z= 0.204 Angle : 0.698 9.681 4377 Z= 0.353 Chirality : 0.047 0.181 479 Planarity : 0.006 0.101 561 Dihedral : 6.561 42.105 463 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.50 % Favored : 85.50 % Rotamer: Outliers : 1.48 % Allowed : 14.50 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -3.38 (0.42), residues: 393 helix: -5.10 (0.34), residues: 18 sheet: -1.69 (0.48), residues: 116 loop : -2.41 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.000 0.000 HIS A 519 PHE 0.030 0.001 PHE C 71 TYR 0.014 0.001 TYR C 49 ARG 0.008 0.000 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.362 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 48 average time/residue: 0.1427 time to fit residues: 8.5916 Evaluate side-chains 44 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.350 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0342 time to fit residues: 0.6977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3214 Z= 0.274 Angle : 0.717 10.128 4377 Z= 0.362 Chirality : 0.048 0.195 479 Planarity : 0.007 0.104 561 Dihedral : 6.586 41.315 463 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.52 % Favored : 84.48 % Rotamer: Outliers : 1.78 % Allowed : 17.16 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -3.36 (0.42), residues: 393 helix: -5.19 (0.26), residues: 18 sheet: -1.64 (0.49), residues: 116 loop : -2.42 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 436 HIS 0.001 0.000 HIS A 519 PHE 0.036 0.002 PHE C 71 TYR 0.013 0.002 TYR B 59 ARG 0.008 0.001 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.350 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 48 average time/residue: 0.1552 time to fit residues: 9.2967 Evaluate side-chains 48 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.423 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0470 time to fit residues: 1.0143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3214 Z= 0.260 Angle : 0.713 10.745 4377 Z= 0.360 Chirality : 0.047 0.189 479 Planarity : 0.006 0.092 561 Dihedral : 6.551 41.400 463 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.03 % Favored : 83.97 % Rotamer: Outliers : 1.78 % Allowed : 18.93 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 (0.42), residues: 393 helix: -5.19 (0.27), residues: 18 sheet: -1.58 (0.49), residues: 116 loop : -2.41 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 436 HIS 0.001 0.000 HIS A 519 PHE 0.035 0.002 PHE C 71 TYR 0.017 0.002 TYR B 59 ARG 0.007 0.000 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.344 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 47 average time/residue: 0.1514 time to fit residues: 8.8016 Evaluate side-chains 43 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.320 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0319 time to fit residues: 0.6060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 0.0970 chunk 37 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 19 optimal weight: 0.9990 chunk 36 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 3214 Z= 0.232 Angle : 0.701 11.487 4377 Z= 0.351 Chirality : 0.047 0.181 479 Planarity : 0.006 0.073 561 Dihedral : 6.198 39.251 463 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.76 % Favored : 85.24 % Rotamer: Outliers : 2.37 % Allowed : 21.30 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -3.20 (0.42), residues: 393 helix: -5.09 (0.35), residues: 18 sheet: -1.39 (0.50), residues: 116 loop : -2.37 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.000 0.000 HIS A 519 PHE 0.029 0.001 PHE C 71 TYR 0.013 0.001 TYR C 49 ARG 0.005 0.000 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.342 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 50 average time/residue: 0.1625 time to fit residues: 10.0712 Evaluate side-chains 47 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.350 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0346 time to fit residues: 0.6839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 18 optimal weight: 0.0870 overall best weight: 0.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 3214 Z= 0.329 Angle : 0.760 11.207 4377 Z= 0.385 Chirality : 0.050 0.210 479 Planarity : 0.006 0.065 561 Dihedral : 6.622 39.853 463 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.30 % Favored : 82.70 % Rotamer: Outliers : 1.48 % Allowed : 19.82 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 (0.42), residues: 393 helix: -5.19 (0.27), residues: 18 sheet: -1.65 (0.47), residues: 126 loop : -2.38 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 112 HIS 0.001 0.001 HIS A 519 PHE 0.041 0.002 PHE C 71 TYR 0.013 0.002 TYR C 49 ARG 0.003 0.000 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.376 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 50 average time/residue: 0.1612 time to fit residues: 10.0850 Evaluate side-chains 48 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.361 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0347 time to fit residues: 0.6716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 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 39 GLN ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3214 Z= 0.277 Angle : 0.736 11.626 4377 Z= 0.372 Chirality : 0.048 0.190 479 Planarity : 0.005 0.052 561 Dihedral : 6.482 40.276 463 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.79 % Favored : 83.21 % Rotamer: Outliers : 1.78 % Allowed : 20.71 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -3.19 (0.42), residues: 393 helix: -5.14 (0.29), residues: 18 sheet: -1.39 (0.49), residues: 121 loop : -2.38 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 436 HIS 0.000 0.000 HIS A 519 PHE 0.038 0.002 PHE C 71 TYR 0.013 0.001 TYR C 49 ARG 0.002 0.000 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.352 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 46 average time/residue: 0.1669 time to fit residues: 9.4727 Evaluate side-chains 47 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.345 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0361 time to fit residues: 0.7959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.0980 chunk 34 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 0.0000 chunk 25 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 30 optimal weight: 0.0770 chunk 3 optimal weight: 1.9990 overall best weight: 0.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3214 Z= 0.210 Angle : 0.694 12.496 4377 Z= 0.349 Chirality : 0.047 0.177 479 Planarity : 0.005 0.044 561 Dihedral : 6.044 36.947 463 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.03 % Favored : 83.97 % Rotamer: Outliers : 0.00 % Allowed : 22.78 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -3.12 (0.42), residues: 393 helix: -5.11 (0.31), residues: 18 sheet: -1.35 (0.50), residues: 115 loop : -2.31 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 436 HIS 0.000 0.000 HIS A 519 PHE 0.032 0.001 PHE C 71 TYR 0.014 0.001 TYR C 49 ARG 0.002 0.000 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.367 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1595 time to fit residues: 8.5029 Evaluate side-chains 41 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.332 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 0.0670 chunk 12 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3214 Z= 0.240 Angle : 0.701 11.804 4377 Z= 0.352 Chirality : 0.048 0.186 479 Planarity : 0.005 0.043 561 Dihedral : 6.132 37.138 463 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.78 % Favored : 84.22 % Rotamer: Outliers : 0.59 % Allowed : 22.49 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -3.10 (0.42), residues: 393 helix: -5.12 (0.29), residues: 18 sheet: -1.31 (0.50), residues: 115 loop : -2.30 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 112 HIS 0.000 0.000 HIS A 519 PHE 0.035 0.002 PHE C 71 TYR 0.014 0.001 TYR B 59 ARG 0.003 0.000 ARG B 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.370 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 44 average time/residue: 0.1827 time to fit residues: 9.8224 Evaluate side-chains 44 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.342 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0364 time to fit residues: 0.5348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.151097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.138227 restraints weight = 4633.904| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 1.64 r_work: 0.3707 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3214 Z= 0.286 Angle : 0.736 11.605 4377 Z= 0.371 Chirality : 0.049 0.195 479 Planarity : 0.005 0.044 561 Dihedral : 6.373 37.504 463 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.25 % Allowed : 16.03 % Favored : 83.72 % Rotamer: Outliers : 0.30 % Allowed : 22.49 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -3.11 (0.42), residues: 393 helix: -5.13 (0.27), residues: 18 sheet: -1.35 (0.48), residues: 120 loop : -2.30 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 112 HIS 0.001 0.000 HIS A 519 PHE 0.041 0.002 PHE C 71 TYR 0.014 0.002 TYR C 49 ARG 0.002 0.000 ARG B 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1306.86 seconds wall clock time: 24 minutes 17.97 seconds (1457.97 seconds total)