Starting phenix.real_space_refine on Tue Feb 13 05:07:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1n_35928/02_2024/8j1n_35928_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1n_35928/02_2024/8j1n_35928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1n_35928/02_2024/8j1n_35928.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1n_35928/02_2024/8j1n_35928.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1n_35928/02_2024/8j1n_35928_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1n_35928/02_2024/8j1n_35928_updated.pdb" } resolution = 2.51 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= 0.146 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 18 5.16 5 C 2106 2.51 5 N 545 2.21 5 O 619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 83": "NH1" <-> "NH2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "A ARG 293": "NH1" <-> "NH2" Residue "B GLU 6": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 3292 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2180 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 274} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 997 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "A" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 115 Unusual residues: {'CDL': 1, 'DNF': 1, 'PC1': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 102 Time building chain proxies: 2.69, per 1000 atoms: 0.82 Number of scatterers: 3292 At special positions: 0 Unit cell: (66.72, 68.388, 110.922, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 4 15.00 O 619 8.00 N 545 7.00 C 2106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 750.9 milliseconds 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 754 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 14 helices and 4 sheets defined 56.3% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 12 through 42 Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 57 through 68 Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 77 through 106 removed outlier: 4.129A pdb=" N PHE A 101 " --> pdb=" O THR A 97 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 142 Proline residue: A 132 - end of helix Processing helix chain 'A' and resid 156 through 167 Processing helix chain 'A' and resid 169 through 173 Processing helix chain 'A' and resid 176 through 204 Processing helix chain 'A' and resid 211 through 241 Proline residue: A 231 - end of helix Processing helix chain 'A' and resid 250 through 261 Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 270 through 296 Processing helix chain 'B' and resid 29 through 31 No H-bonds generated for 'chain 'B' and resid 29 through 31' Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'B' and resid 3 through 7 Processing sheet with id= B, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.224A pdb=" N THR B 118 " --> pdb=" O VAL B 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 115 through 117 removed outlier: 6.024A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 97 through 100 209 hydrogen bonds defined for protein. 597 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: 0.83 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 517 1.30 - 1.43: 891 1.43 - 1.56: 1920 1.56 - 1.69: 8 1.69 - 1.81: 27 Bond restraints: 3363 Sorted by residual: bond pdb=" CA7 CDL A 402 " pdb=" OA8 CDL A 402 " ideal model delta sigma weight residual 1.334 1.457 -0.123 1.10e-02 8.26e+03 1.26e+02 bond pdb=" CB7 CDL A 402 " pdb=" OB8 CDL A 402 " ideal model delta sigma weight residual 1.334 1.442 -0.108 1.10e-02 8.26e+03 9.61e+01 bond pdb=" CA5 CDL A 402 " pdb=" OA6 CDL A 402 " ideal model delta sigma weight residual 1.342 1.458 -0.116 1.50e-02 4.44e+03 5.93e+01 bond pdb=" CB5 CDL A 402 " pdb=" OB6 CDL A 402 " ideal model delta sigma weight residual 1.342 1.445 -0.103 1.50e-02 4.44e+03 4.74e+01 bond pdb=" C21 PC1 A 403 " pdb=" O21 PC1 A 403 " ideal model delta sigma weight residual 1.331 1.457 -0.126 2.00e-02 2.50e+03 3.96e+01 ... (remaining 3358 not shown) Histogram of bond angle deviations from ideal: 98.13 - 105.32: 64 105.32 - 112.52: 1769 112.52 - 119.72: 1078 119.72 - 126.92: 1599 126.92 - 134.11: 49 Bond angle restraints: 4559 Sorted by residual: angle pdb=" C51 CDL A 402 " pdb=" CB5 CDL A 402 " pdb=" OB6 CDL A 402 " ideal model delta sigma weight residual 111.33 120.79 -9.46 1.32e+00 5.72e-01 5.12e+01 angle pdb=" C11 CDL A 402 " pdb=" CA5 CDL A 402 " pdb=" OA6 CDL A 402 " ideal model delta sigma weight residual 111.33 120.58 -9.25 1.32e+00 5.72e-01 4.90e+01 angle pdb=" C71 CDL A 402 " pdb=" CB7 CDL A 402 " pdb=" OB8 CDL A 402 " ideal model delta sigma weight residual 111.64 121.39 -9.75 1.65e+00 3.69e-01 3.51e+01 angle pdb=" C31 CDL A 402 " pdb=" CA7 CDL A 402 " pdb=" OA8 CDL A 402 " ideal model delta sigma weight residual 111.64 120.78 -9.14 1.65e+00 3.69e-01 3.08e+01 angle pdb=" OB6 CDL A 402 " pdb=" CB5 CDL A 402 " pdb=" OB7 CDL A 402 " ideal model delta sigma weight residual 123.92 118.75 5.17 1.00e+00 9.92e-01 2.65e+01 ... (remaining 4554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.92: 1835 20.92 - 41.84: 122 41.84 - 62.75: 34 62.75 - 83.67: 4 83.67 - 104.59: 4 Dihedral angle restraints: 1999 sinusoidal: 816 harmonic: 1183 Sorted by residual: dihedral pdb=" CA ARG B 72 " pdb=" C ARG B 72 " pdb=" N ASP B 73 " pdb=" CA ASP B 73 " ideal model delta harmonic sigma weight residual 180.00 155.64 24.36 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA5 CDL A 402 " pdb=" CA4 CDL A 402 " pdb=" OA6 CDL A 402 " pdb=" CA6 CDL A 402 " ideal model delta sinusoidal sigma weight residual 168.24 63.65 104.59 1 3.00e+01 1.11e-03 1.34e+01 dihedral pdb=" CA TRP B 111 " pdb=" C TRP B 111 " pdb=" N GLY B 112 " pdb=" CA GLY B 112 " ideal model delta harmonic sigma weight residual 180.00 163.83 16.17 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 1996 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 337 0.045 - 0.090: 132 0.090 - 0.135: 33 0.135 - 0.180: 3 0.180 - 0.225: 1 Chirality restraints: 506 Sorted by residual: chirality pdb=" CB ILE A 116 " pdb=" CA ILE A 116 " pdb=" CG1 ILE A 116 " pdb=" CG2 ILE A 116 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA VAL A 211 " pdb=" N VAL A 211 " pdb=" C VAL A 211 " pdb=" CB VAL A 211 " both_signs ideal model delta sigma weight residual False 2.44 2.30 0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CG LEU A 90 " pdb=" CB LEU A 90 " pdb=" CD1 LEU A 90 " pdb=" CD2 LEU A 90 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 503 not shown) Planarity restraints: 569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 101 " 0.025 2.00e-02 2.50e+03 3.82e-02 2.55e+01 pdb=" CG PHE B 101 " -0.086 2.00e-02 2.50e+03 pdb=" CD1 PHE B 101 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 PHE B 101 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 PHE B 101 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE B 101 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 101 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 27 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO B 28 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 28 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 28 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 96 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.82e+00 pdb=" C ASP A 96 " 0.023 2.00e-02 2.50e+03 pdb=" O ASP A 96 " -0.009 2.00e-02 2.50e+03 pdb=" N THR A 97 " -0.008 2.00e-02 2.50e+03 ... (remaining 566 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 506 2.76 - 3.29: 3120 3.29 - 3.83: 6015 3.83 - 4.36: 6948 4.36 - 4.90: 11954 Nonbonded interactions: 28543 Sorted by model distance: nonbonded pdb=" O TRP A 173 " pdb=" OG1 THR A 176 " model vdw 2.219 2.440 nonbonded pdb=" OG1 THR A 30 " pdb=" NH1 ARG A 276 " model vdw 2.233 2.520 nonbonded pdb=" O GLY A 130 " pdb=" OG1 THR A 133 " model vdw 2.300 2.440 nonbonded pdb=" O ALA A 63 " pdb=" OG1 THR A 67 " model vdw 2.342 2.440 nonbonded pdb=" OE2 GLU B 6 " pdb=" N CYS B 96 " model vdw 2.353 2.520 ... (remaining 28538 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.970 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.340 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.010 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:11.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 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 : 0.009 0.126 3363 Z= 0.583 Angle : 1.010 9.745 4559 Z= 0.523 Chirality : 0.049 0.225 506 Planarity : 0.005 0.038 569 Dihedral : 15.984 104.588 1242 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % 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 : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.39), residues: 410 helix: 1.87 (0.32), residues: 223 sheet: -0.02 (0.64), residues: 59 loop : 0.60 (0.54), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 56 HIS 0.004 0.001 HIS A 214 PHE 0.086 0.004 PHE B 101 TYR 0.020 0.002 TYR A 157 ARG 0.008 0.001 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.360 Fit side-chains REVERT: A 157 TYR cc_start: 0.7543 (m-80) cc_final: 0.6787 (t80) REVERT: A 169 LEU cc_start: 0.8127 (mm) cc_final: 0.7893 (mt) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.9552 time to fit residues: 68.2901 Evaluate side-chains 61 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7639 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3363 Z= 0.219 Angle : 0.552 6.843 4559 Z= 0.285 Chirality : 0.041 0.183 506 Planarity : 0.004 0.043 569 Dihedral : 12.535 85.163 535 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.78 % Allowed : 10.65 % Favored : 87.57 % 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: 2.26 (0.40), residues: 410 helix: 2.54 (0.32), residues: 223 sheet: -0.09 (0.64), residues: 54 loop : 0.47 (0.52), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 111 HIS 0.003 0.001 HIS B 35 PHE 0.031 0.002 PHE B 101 TYR 0.012 0.001 TYR A 157 ARG 0.005 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.384 Fit side-chains REVERT: A 150 LYS cc_start: 0.8214 (tptp) cc_final: 0.7951 (tttm) REVERT: A 157 TYR cc_start: 0.7379 (m-80) cc_final: 0.6701 (t80) REVERT: A 169 LEU cc_start: 0.8197 (mm) cc_final: 0.7953 (mt) REVERT: B 83 MET cc_start: 0.7795 (mtp) cc_final: 0.7593 (mtp) outliers start: 6 outliers final: 1 residues processed: 62 average time/residue: 0.9981 time to fit residues: 64.0989 Evaluate side-chains 56 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 25 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 290 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3363 Z= 0.246 Angle : 0.552 6.618 4559 Z= 0.285 Chirality : 0.041 0.179 506 Planarity : 0.004 0.033 569 Dihedral : 12.251 80.626 535 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.07 % Allowed : 13.61 % Favored : 84.32 % 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: 2.41 (0.40), residues: 410 helix: 2.65 (0.32), residues: 223 sheet: 0.08 (0.64), residues: 54 loop : 0.51 (0.53), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 56 HIS 0.004 0.001 HIS B 35 PHE 0.015 0.002 PHE B 101 TYR 0.015 0.001 TYR A 157 ARG 0.003 0.001 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.383 Fit side-chains REVERT: A 150 LYS cc_start: 0.8246 (tptp) cc_final: 0.7975 (tttm) REVERT: A 157 TYR cc_start: 0.7430 (m-80) cc_final: 0.6754 (t80) REVERT: A 169 LEU cc_start: 0.8214 (mm) cc_final: 0.7961 (mt) outliers start: 7 outliers final: 3 residues processed: 60 average time/residue: 0.9522 time to fit residues: 59.3031 Evaluate side-chains 57 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 35 optimal weight: 6.9990 chunk 10 optimal weight: 0.0010 chunk 33 optimal weight: 0.9980 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3363 Z= 0.171 Angle : 0.494 6.460 4559 Z= 0.253 Chirality : 0.039 0.178 506 Planarity : 0.004 0.030 569 Dihedral : 11.849 79.681 535 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.07 % Allowed : 14.20 % Favored : 83.73 % 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: 2.86 (0.40), residues: 410 helix: 3.02 (0.32), residues: 223 sheet: 0.37 (0.64), residues: 54 loop : 0.66 (0.54), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 111 HIS 0.003 0.001 HIS B 35 PHE 0.008 0.001 PHE A 128 TYR 0.010 0.001 TYR A 157 ARG 0.003 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 51 time to evaluate : 0.379 Fit side-chains REVERT: A 116 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7653 (mp) REVERT: A 150 LYS cc_start: 0.8255 (tptp) cc_final: 0.7997 (tttm) REVERT: A 157 TYR cc_start: 0.7260 (m-80) cc_final: 0.6654 (t80) REVERT: A 169 LEU cc_start: 0.8227 (mm) cc_final: 0.7961 (mt) REVERT: A 187 ASN cc_start: 0.8039 (t0) cc_final: 0.7306 (m-40) REVERT: A 219 LEU cc_start: 0.8014 (tp) cc_final: 0.7505 (tp) REVERT: B 83 MET cc_start: 0.7841 (mtp) cc_final: 0.7612 (mtp) outliers start: 7 outliers final: 2 residues processed: 55 average time/residue: 1.1184 time to fit residues: 63.5053 Evaluate side-chains 53 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 16 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3363 Z= 0.212 Angle : 0.524 6.367 4559 Z= 0.267 Chirality : 0.040 0.194 506 Planarity : 0.004 0.030 569 Dihedral : 11.841 79.643 535 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.07 % Allowed : 15.38 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.40), residues: 410 helix: 3.07 (0.32), residues: 223 sheet: 0.41 (0.63), residues: 54 loop : 0.64 (0.53), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 56 HIS 0.004 0.001 HIS B 59 PHE 0.011 0.002 PHE A 128 TYR 0.014 0.001 TYR A 157 ARG 0.005 0.000 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.359 Fit side-chains REVERT: A 116 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7612 (mp) REVERT: A 150 LYS cc_start: 0.8233 (tptp) cc_final: 0.7969 (tttm) REVERT: A 157 TYR cc_start: 0.7359 (m-80) cc_final: 0.6717 (t80) REVERT: A 169 LEU cc_start: 0.8220 (mm) cc_final: 0.7954 (mt) REVERT: B 83 MET cc_start: 0.7921 (mtp) cc_final: 0.7569 (mtp) outliers start: 7 outliers final: 3 residues processed: 62 average time/residue: 0.9672 time to fit residues: 62.1913 Evaluate side-chains 61 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3363 Z= 0.210 Angle : 0.523 6.340 4559 Z= 0.266 Chirality : 0.040 0.207 506 Planarity : 0.004 0.030 569 Dihedral : 11.801 79.700 535 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.66 % Allowed : 15.09 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.40), residues: 410 helix: 3.14 (0.32), residues: 222 sheet: 0.49 (0.64), residues: 54 loop : 0.67 (0.54), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 56 HIS 0.004 0.001 HIS B 35 PHE 0.010 0.001 PHE A 128 TYR 0.013 0.001 TYR A 157 ARG 0.003 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 0.383 Fit side-chains REVERT: A 116 ILE cc_start: 0.7934 (OUTLIER) cc_final: 0.7633 (mp) REVERT: A 150 LYS cc_start: 0.8225 (tptp) cc_final: 0.7970 (tttm) REVERT: A 157 TYR cc_start: 0.7361 (m-80) cc_final: 0.6721 (t80) REVERT: A 169 LEU cc_start: 0.8215 (mm) cc_final: 0.7948 (mt) REVERT: B 83 MET cc_start: 0.7971 (mtp) cc_final: 0.7677 (mtp) outliers start: 9 outliers final: 4 residues processed: 65 average time/residue: 0.9683 time to fit residues: 65.2344 Evaluate side-chains 63 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 58 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 25 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.7653 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3363 Z= 0.179 Angle : 0.520 10.085 4559 Z= 0.260 Chirality : 0.040 0.242 506 Planarity : 0.004 0.029 569 Dihedral : 11.584 78.276 535 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.07 % Allowed : 15.98 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.10 (0.40), residues: 410 helix: 3.23 (0.32), residues: 222 sheet: 0.57 (0.63), residues: 54 loop : 0.71 (0.54), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 111 HIS 0.003 0.001 HIS B 35 PHE 0.009 0.001 PHE A 128 TYR 0.011 0.001 TYR A 157 ARG 0.003 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.344 Fit side-chains REVERT: A 116 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7591 (mp) REVERT: A 150 LYS cc_start: 0.8246 (tptp) cc_final: 0.7992 (tttm) REVERT: A 157 TYR cc_start: 0.7300 (m-80) cc_final: 0.6683 (t80) REVERT: A 169 LEU cc_start: 0.8213 (mm) cc_final: 0.7934 (mt) REVERT: A 187 ASN cc_start: 0.8075 (t0) cc_final: 0.7359 (m-40) REVERT: B 83 MET cc_start: 0.7978 (mtp) cc_final: 0.7689 (mtp) outliers start: 7 outliers final: 2 residues processed: 61 average time/residue: 0.8882 time to fit residues: 56.3359 Evaluate side-chains 58 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 0.0570 chunk 31 optimal weight: 0.4980 chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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: 0.7662 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3363 Z= 0.193 Angle : 0.527 8.067 4559 Z= 0.265 Chirality : 0.040 0.255 506 Planarity : 0.004 0.030 569 Dihedral : 11.535 76.164 535 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.37 % Allowed : 15.98 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.07 (0.40), residues: 410 helix: 3.18 (0.32), residues: 222 sheet: 0.59 (0.64), residues: 54 loop : 0.73 (0.54), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 56 HIS 0.003 0.001 HIS B 35 PHE 0.010 0.001 PHE A 223 TYR 0.012 0.001 TYR A 157 ARG 0.003 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 59 time to evaluate : 0.317 Fit side-chains REVERT: A 115 LYS cc_start: 0.7663 (mtpt) cc_final: 0.7431 (mtmt) REVERT: A 116 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7558 (mp) REVERT: A 150 LYS cc_start: 0.8220 (tptp) cc_final: 0.7977 (tttm) REVERT: A 157 TYR cc_start: 0.7313 (m-80) cc_final: 0.6707 (t80) REVERT: A 169 LEU cc_start: 0.8192 (mm) cc_final: 0.7910 (mt) REVERT: A 255 MET cc_start: 0.8938 (tpt) cc_final: 0.8679 (tpt) outliers start: 8 outliers final: 3 residues processed: 63 average time/residue: 0.9531 time to fit residues: 62.3007 Evaluate side-chains 61 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 0.0770 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 0.0980 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3363 Z= 0.182 Angle : 0.526 9.459 4559 Z= 0.261 Chirality : 0.040 0.256 506 Planarity : 0.004 0.029 569 Dihedral : 11.420 74.815 535 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.48 % Allowed : 16.86 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.14 (0.40), residues: 410 helix: 3.25 (0.32), residues: 222 sheet: 0.62 (0.63), residues: 54 loop : 0.74 (0.54), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 111 HIS 0.003 0.001 HIS B 35 PHE 0.009 0.001 PHE A 128 TYR 0.012 0.001 TYR A 157 ARG 0.003 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 0.365 Fit side-chains REVERT: A 115 LYS cc_start: 0.7649 (mtpt) cc_final: 0.7405 (mtmt) REVERT: A 116 ILE cc_start: 0.7892 (OUTLIER) cc_final: 0.7563 (mp) REVERT: A 150 LYS cc_start: 0.8220 (tptp) cc_final: 0.7977 (tttm) REVERT: A 157 TYR cc_start: 0.7297 (m-80) cc_final: 0.6674 (t80) REVERT: A 169 LEU cc_start: 0.8181 (mm) cc_final: 0.7903 (mt) REVERT: A 187 ASN cc_start: 0.8057 (t0) cc_final: 0.7334 (m-40) outliers start: 5 outliers final: 4 residues processed: 63 average time/residue: 0.9192 time to fit residues: 60.1614 Evaluate side-chains 62 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 0.3980 chunk 25 optimal weight: 0.3980 chunk 19 optimal weight: 0.0370 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3363 Z= 0.165 Angle : 0.517 8.955 4559 Z= 0.257 Chirality : 0.039 0.253 506 Planarity : 0.004 0.029 569 Dihedral : 11.301 73.278 535 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.18 % Allowed : 17.75 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.20 (0.40), residues: 410 helix: 3.28 (0.32), residues: 222 sheet: 0.67 (0.63), residues: 54 loop : 0.79 (0.54), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 111 HIS 0.003 0.001 HIS B 35 PHE 0.008 0.001 PHE A 128 TYR 0.011 0.001 TYR B 95 ARG 0.003 0.000 ARG B 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.362 Fit side-chains REVERT: A 115 LYS cc_start: 0.7618 (mtpt) cc_final: 0.7372 (mtmt) REVERT: A 116 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7530 (mp) REVERT: A 150 LYS cc_start: 0.8221 (tptp) cc_final: 0.7983 (tttp) REVERT: A 157 TYR cc_start: 0.7232 (m-80) cc_final: 0.6663 (t80) REVERT: A 169 LEU cc_start: 0.8193 (mm) cc_final: 0.7909 (mt) REVERT: A 187 ASN cc_start: 0.8023 (t0) cc_final: 0.7306 (m-40) outliers start: 4 outliers final: 3 residues processed: 61 average time/residue: 0.8922 time to fit residues: 56.6357 Evaluate side-chains 61 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 0.4980 chunk 24 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 214 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.174467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.126066 restraints weight = 3171.897| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.14 r_work: 0.3174 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3363 Z= 0.196 Angle : 0.534 9.120 4559 Z= 0.267 Chirality : 0.040 0.261 506 Planarity : 0.004 0.029 569 Dihedral : 11.407 72.559 535 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.18 % Allowed : 18.05 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.12 (0.40), residues: 410 helix: 3.20 (0.32), residues: 222 sheet: 0.67 (0.63), residues: 54 loop : 0.75 (0.54), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 111 HIS 0.003 0.001 HIS B 35 PHE 0.010 0.001 PHE A 128 TYR 0.012 0.001 TYR A 157 ARG 0.003 0.000 ARG B 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1799.40 seconds wall clock time: 32 minutes 57.43 seconds (1977.43 seconds total)