Starting phenix.real_space_refine on Sun Mar 10 17:24:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adu_15370/03_2024/8adu_15370.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adu_15370/03_2024/8adu_15370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adu_15370/03_2024/8adu_15370.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adu_15370/03_2024/8adu_15370.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adu_15370/03_2024/8adu_15370.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adu_15370/03_2024/8adu_15370.pdb" } resolution = 3.24 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= 0.008 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 10 5.16 5 C 2160 2.51 5 N 600 2.21 5 O 690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3460 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Chain: "B" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Chain: "C" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Chain: "D" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Chain: "E" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Time building chain proxies: 2.21, per 1000 atoms: 0.64 Number of scatterers: 3460 At special positions: 0 Unit cell: (86.1, 97.65, 39.9, 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 10 16.00 O 690 8.00 N 600 7.00 C 2160 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.32 Conformation dependent library (CDL) restraints added in 1.0 seconds 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 850 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 20 removed outlier: 6.880A pdb=" N ALA A 17 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N GLU B 20 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA A 19 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA B 17 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N GLU C 20 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA B 19 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA C 17 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N GLU D 20 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA C 19 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA D 17 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N GLU E 20 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA D 19 " --> pdb=" O GLU E 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 31 Processing sheet with id=AA3, first strand: chain 'A' and resid 38 through 40 Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 54 Processing sheet with id=AA5, first strand: chain 'A' and resid 61 through 66 removed outlier: 6.207A pdb=" N GLN A 62 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ASN B 65 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR A 64 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLN B 62 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ASN C 65 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR B 64 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLN C 62 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ASN D 65 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR C 64 " --> pdb=" O ASN D 65 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLN D 62 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ASN E 65 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N THR D 64 " --> pdb=" O ASN E 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 69 through 71 Processing sheet with id=AA7, first strand: chain 'A' and resid 75 through 78 Processing sheet with id=AA8, first strand: chain 'A' and resid 92 through 94 76 hydrogen bonds defined for protein. 228 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.77 Time building geometry restraints manager: 1.42 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: 1145 1.34 - 1.45: 439 1.45 - 1.57: 1871 1.57 - 1.69: 0 1.69 - 1.80: 20 Bond restraints: 3475 Sorted by residual: bond pdb=" CB VAL E 15 " pdb=" CG2 VAL E 15 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.70e+00 bond pdb=" CB VAL A 15 " pdb=" CG2 VAL A 15 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.69e+00 bond pdb=" CB VAL D 15 " pdb=" CG2 VAL D 15 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.67e+00 bond pdb=" CB VAL C 15 " pdb=" CG2 VAL C 15 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.67e+00 bond pdb=" CB VAL B 15 " pdb=" CG2 VAL B 15 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.66e+00 ... (remaining 3470 not shown) Histogram of bond angle deviations from ideal: 100.53 - 106.67: 35 106.67 - 112.80: 2045 112.80 - 118.94: 867 118.94 - 125.08: 1708 125.08 - 131.22: 5 Bond angle restraints: 4660 Sorted by residual: angle pdb=" CA GLN D 79 " pdb=" CB GLN D 79 " pdb=" CG GLN D 79 " ideal model delta sigma weight residual 114.10 118.52 -4.42 2.00e+00 2.50e-01 4.87e+00 angle pdb=" CA GLN A 79 " pdb=" CB GLN A 79 " pdb=" CG GLN A 79 " ideal model delta sigma weight residual 114.10 118.51 -4.41 2.00e+00 2.50e-01 4.86e+00 angle pdb=" C GLN E 79 " pdb=" CA GLN E 79 " pdb=" CB GLN E 79 " ideal model delta sigma weight residual 110.42 114.81 -4.39 1.99e+00 2.53e-01 4.86e+00 angle pdb=" CA GLN C 79 " pdb=" CB GLN C 79 " pdb=" CG GLN C 79 " ideal model delta sigma weight residual 114.10 118.50 -4.40 2.00e+00 2.50e-01 4.85e+00 angle pdb=" C GLN C 79 " pdb=" CA GLN C 79 " pdb=" CB GLN C 79 " ideal model delta sigma weight residual 110.42 114.80 -4.38 1.99e+00 2.53e-01 4.85e+00 ... (remaining 4655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 1904 17.35 - 34.69: 136 34.69 - 52.03: 30 52.03 - 69.38: 5 69.38 - 86.72: 15 Dihedral angle restraints: 2090 sinusoidal: 745 harmonic: 1345 Sorted by residual: dihedral pdb=" CA MET E 5 " pdb=" C MET E 5 " pdb=" N LYS E 6 " pdb=" CA LYS E 6 " ideal model delta harmonic sigma weight residual 180.00 -160.26 -19.74 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA MET D 5 " pdb=" C MET D 5 " pdb=" N LYS D 6 " pdb=" CA LYS D 6 " ideal model delta harmonic sigma weight residual -180.00 -160.27 -19.73 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA MET C 5 " pdb=" C MET C 5 " pdb=" N LYS C 6 " pdb=" CA LYS C 6 " ideal model delta harmonic sigma weight residual -180.00 -160.27 -19.73 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 2087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 505 0.087 - 0.173: 65 0.173 - 0.260: 5 0.260 - 0.347: 0 0.347 - 0.433: 5 Chirality restraints: 580 Sorted by residual: chirality pdb=" CB VAL D 15 " pdb=" CA VAL D 15 " pdb=" CG1 VAL D 15 " pdb=" CG2 VAL D 15 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.70e+00 chirality pdb=" CB VAL E 15 " pdb=" CA VAL E 15 " pdb=" CG1 VAL E 15 " pdb=" CG2 VAL E 15 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.65e+00 chirality pdb=" CB VAL B 15 " pdb=" CA VAL B 15 " pdb=" CG1 VAL B 15 " pdb=" CG2 VAL B 15 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.65e+00 ... (remaining 577 not shown) Planarity restraints: 585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 4 " -0.010 2.00e-02 2.50e+03 9.37e-03 1.54e+00 pdb=" CG PHE E 4 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE E 4 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE E 4 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE E 4 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE E 4 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE E 4 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 4 " -0.010 2.00e-02 2.50e+03 9.22e-03 1.49e+00 pdb=" CG PHE D 4 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE D 4 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE D 4 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE D 4 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 4 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE D 4 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 4 " -0.010 2.00e-02 2.50e+03 9.20e-03 1.48e+00 pdb=" CG PHE C 4 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE C 4 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE C 4 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE C 4 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 4 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 4 " -0.003 2.00e-02 2.50e+03 ... (remaining 582 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1071 2.82 - 3.34: 3134 3.34 - 3.86: 5731 3.86 - 4.38: 6806 4.38 - 4.90: 13256 Nonbonded interactions: 29998 Sorted by model distance: nonbonded pdb=" OG SER E 9 " pdb=" N LYS E 10 " model vdw 2.296 2.520 nonbonded pdb=" OG SER C 9 " pdb=" N LYS C 10 " model vdw 2.297 2.520 nonbonded pdb=" OG SER D 9 " pdb=" N LYS D 10 " model vdw 2.297 2.520 nonbonded pdb=" OG SER A 9 " pdb=" N LYS A 10 " model vdw 2.297 2.520 nonbonded pdb=" OG SER B 9 " pdb=" N LYS B 10 " model vdw 2.297 2.520 ... (remaining 29993 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.770 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: 3.280 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.510 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 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 : 0.007 0.057 3475 Z= 0.458 Angle : 0.820 4.415 4660 Z= 0.461 Chirality : 0.068 0.433 580 Planarity : 0.003 0.009 585 Dihedral : 15.523 86.720 1240 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.34 % Favored : 88.66 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.91 (0.25), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.74 (0.19), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.022 0.005 PHE E 4 TYR 0.005 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 LYS cc_start: 0.7926 (tttm) cc_final: 0.7706 (ttmm) REVERT: B 99 GLN cc_start: 0.4969 (tm-30) cc_final: 0.4709 (tm-30) REVERT: C 12 LYS cc_start: 0.7500 (mptt) cc_final: 0.7264 (mptt) REVERT: C 60 LYS cc_start: 0.7879 (tttm) cc_final: 0.7641 (ttmm) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1372 time to fit residues: 15.2306 Evaluate side-chains 69 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 11 optimal weight: 0.0970 chunk 23 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3475 Z= 0.307 Angle : 0.656 7.203 4660 Z= 0.351 Chirality : 0.051 0.167 580 Planarity : 0.003 0.010 585 Dihedral : 5.224 19.701 495 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.78 % Favored : 87.22 % Rotamer: Outliers : 6.67 % Allowed : 15.36 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.49 (0.28), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.22), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.020 0.005 PHE D 4 TYR 0.012 0.002 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 77 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.5074 (tm-30) cc_final: 0.4821 (tm-30) REVERT: B 2 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7334 (m-30) REVERT: B 35 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7694 (tt0) REVERT: E 12 LYS cc_start: 0.7360 (mptt) cc_final: 0.6855 (mmtp) outliers start: 23 outliers final: 16 residues processed: 86 average time/residue: 0.1352 time to fit residues: 14.5728 Evaluate side-chains 89 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 71 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 81 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 12 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 3475 Z= 0.477 Angle : 0.740 6.639 4660 Z= 0.396 Chirality : 0.053 0.161 580 Planarity : 0.003 0.010 585 Dihedral : 5.792 21.241 495 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.58 % Favored : 87.42 % Rotamer: Outliers : 8.70 % Allowed : 15.65 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.48 (0.29), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.22), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.023 0.006 PHE B 94 TYR 0.014 0.003 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 77 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 99 GLN cc_start: 0.5013 (tm-30) cc_final: 0.4755 (tm-30) REVERT: B 2 ASP cc_start: 0.7649 (OUTLIER) cc_final: 0.7209 (m-30) REVERT: B 35 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7604 (tt0) REVERT: C 46 GLU cc_start: 0.8717 (pm20) cc_final: 0.8513 (pm20) REVERT: D 60 LYS cc_start: 0.8071 (tttm) cc_final: 0.7835 (ttmm) outliers start: 30 outliers final: 20 residues processed: 93 average time/residue: 0.1437 time to fit residues: 16.4952 Evaluate side-chains 94 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 72 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 81 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 0.3980 chunk 19 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 43 optimal weight: 0.1980 chunk 21 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 GLN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3475 Z= 0.178 Angle : 0.558 6.585 4660 Z= 0.299 Chirality : 0.048 0.136 580 Planarity : 0.002 0.009 585 Dihedral : 4.698 17.476 495 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.99 % Favored : 87.01 % Rotamer: Outliers : 5.51 % Allowed : 20.58 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.36 (0.29), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.22), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.016 0.004 PHE D 4 TYR 0.017 0.003 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: B 60 LYS cc_start: 0.8055 (tttm) cc_final: 0.7488 (tttm) outliers start: 19 outliers final: 17 residues processed: 90 average time/residue: 0.1462 time to fit residues: 16.1597 Evaluate side-chains 95 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 78 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 59 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 GLN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 3475 Z= 0.481 Angle : 0.742 7.154 4660 Z= 0.395 Chirality : 0.052 0.162 580 Planarity : 0.003 0.011 585 Dihedral : 5.616 20.499 495 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.37 % Favored : 87.63 % Rotamer: Outliers : 8.41 % Allowed : 20.00 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.38 (0.29), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.22), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.024 0.006 PHE B 94 TYR 0.021 0.004 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 74 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 2 ASP cc_start: 0.7672 (OUTLIER) cc_final: 0.7207 (m-30) REVERT: E 10 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7879 (mtpt) outliers start: 29 outliers final: 24 residues processed: 90 average time/residue: 0.1546 time to fit residues: 16.8746 Evaluate side-chains 95 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 69 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 0.4980 chunk 36 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 41 optimal weight: 0.0570 chunk 4 optimal weight: 3.9990 chunk 24 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN C 62 GLN C 79 GLN D 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3475 Z= 0.127 Angle : 0.530 6.188 4660 Z= 0.281 Chirality : 0.049 0.133 580 Planarity : 0.002 0.009 585 Dihedral : 4.398 15.735 495 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.81 % Favored : 86.19 % Rotamer: Outliers : 4.93 % Allowed : 23.48 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.34 (0.29), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.22), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.015 0.003 PHE D 4 TYR 0.007 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.7797 (mptt) cc_final: 0.7120 (tppt) REVERT: E 61 GLU cc_start: 0.7305 (mp0) cc_final: 0.6975 (mp0) outliers start: 17 outliers final: 13 residues processed: 91 average time/residue: 0.1521 time to fit residues: 16.9491 Evaluate side-chains 96 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 81 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 0.3980 chunk 43 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN E 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3475 Z= 0.246 Angle : 0.594 6.730 4660 Z= 0.315 Chirality : 0.049 0.139 580 Planarity : 0.002 0.010 585 Dihedral : 4.520 17.071 495 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.75 % Favored : 88.25 % Rotamer: Outliers : 6.96 % Allowed : 22.61 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.30 (0.29), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.22), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.018 0.004 PHE C 94 TYR 0.010 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 83 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.8702 (pm20) cc_final: 0.8439 (pm20) REVERT: C 99 GLN cc_start: 0.4591 (tm-30) cc_final: 0.4232 (tm-30) REVERT: E 60 LYS cc_start: 0.7662 (ttmm) cc_final: 0.7096 (tttm) outliers start: 24 outliers final: 20 residues processed: 93 average time/residue: 0.1410 time to fit residues: 16.2977 Evaluate side-chains 101 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 81 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 81 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 34 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3475 Z= 0.212 Angle : 0.587 6.835 4660 Z= 0.311 Chirality : 0.049 0.139 580 Planarity : 0.002 0.010 585 Dihedral : 4.470 18.562 495 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.58 % Favored : 87.42 % Rotamer: Outliers : 7.54 % Allowed : 22.32 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.29 (0.30), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.23), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.018 0.004 PHE C 94 TYR 0.009 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 79 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.8683 (pm20) cc_final: 0.8415 (pm20) REVERT: C 99 GLN cc_start: 0.4546 (tm-30) cc_final: 0.4205 (tm-30) outliers start: 26 outliers final: 24 residues processed: 93 average time/residue: 0.1334 time to fit residues: 15.5350 Evaluate side-chains 103 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 79 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 81 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 0.1980 chunk 38 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN E 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 3475 Z= 0.165 Angle : 0.563 6.725 4660 Z= 0.295 Chirality : 0.048 0.138 580 Planarity : 0.002 0.010 585 Dihedral : 4.184 17.541 495 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.75 % Favored : 88.25 % Rotamer: Outliers : 6.09 % Allowed : 25.22 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.24 (0.30), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.23), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.016 0.004 PHE C 94 TYR 0.014 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 80 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.7879 (mptt) cc_final: 0.7175 (tppt) REVERT: B 46 GLU cc_start: 0.8626 (pm20) cc_final: 0.8319 (pm20) REVERT: C 99 GLN cc_start: 0.4621 (tm-30) cc_final: 0.4292 (tm-30) REVERT: D 46 GLU cc_start: 0.8638 (pm20) cc_final: 0.8431 (pm20) outliers start: 21 outliers final: 19 residues processed: 89 average time/residue: 0.1451 time to fit residues: 16.2690 Evaluate side-chains 100 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 81 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 59 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 28 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 5 optimal weight: 0.2980 chunk 9 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3475 Z= 0.156 Angle : 0.580 8.000 4660 Z= 0.296 Chirality : 0.048 0.137 580 Planarity : 0.002 0.010 585 Dihedral : 4.053 18.323 495 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.16 % Favored : 87.84 % Rotamer: Outliers : 5.80 % Allowed : 25.80 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.25 (0.30), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.23), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.017 0.004 PHE C 94 TYR 0.012 0.002 TYR A 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 83 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.7884 (mptt) cc_final: 0.7187 (tppt) REVERT: B 46 GLU cc_start: 0.8625 (pm20) cc_final: 0.8315 (pm20) REVERT: C 99 GLN cc_start: 0.4594 (tm-30) cc_final: 0.4291 (tm-30) REVERT: E 61 GLU cc_start: 0.7335 (mp0) cc_final: 0.6959 (mp0) outliers start: 20 outliers final: 20 residues processed: 90 average time/residue: 0.1292 time to fit residues: 14.6901 Evaluate side-chains 101 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 81 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 59 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 5.9990 chunk 6 optimal weight: 0.4980 chunk 31 optimal weight: 0.3980 chunk 2 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 79 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 = 0.3888 r_free = 0.3888 target = 0.118196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.100191 restraints weight = 4828.887| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.59 r_work: 0.3553 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3475 Z= 0.185 Angle : 0.600 7.662 4660 Z= 0.307 Chirality : 0.048 0.139 580 Planarity : 0.002 0.010 585 Dihedral : 4.125 18.333 495 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.55 % Favored : 88.45 % Rotamer: Outliers : 6.67 % Allowed : 24.93 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.21 (0.30), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.23), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.017 0.004 PHE C 94 TYR 0.014 0.003 TYR A 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1219.43 seconds wall clock time: 22 minutes 48.30 seconds (1368.30 seconds total)