Starting phenix.real_space_refine on Wed Mar 5 22:58:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zam_39880/03_2025/8zam_39880_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zam_39880/03_2025/8zam_39880.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zam_39880/03_2025/8zam_39880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zam_39880/03_2025/8zam_39880.map" model { file = "/net/cci-nas-00/data/ceres_data/8zam_39880/03_2025/8zam_39880_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zam_39880/03_2025/8zam_39880_neut.cif" } resolution = 2.5 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= -0.000 sd= 0.007 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 2 5.49 5 S 34 5.16 5 C 2660 2.51 5 N 634 2.21 5 O 670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4000 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1949 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1949 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'L9Q': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'L9Q': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.82, per 1000 atoms: 2.20 Number of scatterers: 4000 At special positions: 0 Unit cell: (59.85, 75.95, 80.15, 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 34 16.00 P 2 15.00 O 670 8.00 N 634 7.00 C 2660 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 34 " - pdb=" SG CYS B 36 " distance=2.03 Simple disulfide: pdb=" SG CYS A 36 " - pdb=" SG CYS B 34 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.06 Conformation dependent library (CDL) restraints added in 453.1 milliseconds 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 884 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 2 sheets defined 79.3% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 47 through 76 Processing helix chain 'A' and resid 80 through 101 removed outlier: 3.769A pdb=" N ILE A 84 " --> pdb=" O GLY A 80 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 101 " --> pdb=" O GLU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 136 Proline residue: A 129 - end of helix Processing helix chain 'A' and resid 146 through 168 removed outlier: 3.553A pdb=" N MET A 150 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 203 Processing helix chain 'A' and resid 206 through 233 Proline residue: A 227 - end of helix Processing helix chain 'A' and resid 240 through 257 Processing helix chain 'A' and resid 257 through 278 Processing helix chain 'B' and resid 47 through 76 Processing helix chain 'B' and resid 80 through 101 removed outlier: 3.769A pdb=" N ILE B 84 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU B 101 " --> pdb=" O GLU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 136 Proline residue: B 129 - end of helix Processing helix chain 'B' and resid 146 through 168 removed outlier: 3.553A pdb=" N MET B 150 " --> pdb=" O SER B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 203 Processing helix chain 'B' and resid 206 through 233 Proline residue: B 227 - end of helix Processing helix chain 'B' and resid 240 through 257 Processing helix chain 'B' and resid 257 through 278 Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 108 Processing sheet with id=AA2, first strand: chain 'B' and resid 107 through 108 312 hydrogen bonds defined for protein. 930 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: 1.34 Time building geometry restraints manager: 1.25 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: 1125 1.34 - 1.46: 826 1.46 - 1.58: 2115 1.58 - 1.70: 4 1.70 - 1.82: 50 Bond restraints: 4120 Sorted by residual: bond pdb=" C39 L9Q B 401 " pdb=" C40 L9Q B 401 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" C39 L9Q A 401 " pdb=" C40 L9Q A 401 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 9.05e+01 bond pdb=" C11 L9Q B 401 " pdb=" O3 L9Q B 401 " ideal model delta sigma weight residual 1.327 1.456 -0.129 2.00e-02 2.50e+03 4.14e+01 bond pdb=" C31 L9Q B 401 " pdb=" O2 L9Q B 401 " ideal model delta sigma weight residual 1.330 1.455 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" C11 L9Q A 401 " pdb=" O3 L9Q A 401 " ideal model delta sigma weight residual 1.327 1.452 -0.125 2.00e-02 2.50e+03 3.88e+01 ... (remaining 4115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 5534 3.44 - 6.87: 37 6.87 - 10.31: 7 10.31 - 13.75: 2 13.75 - 17.19: 2 Bond angle restraints: 5582 Sorted by residual: angle pdb=" C38 L9Q A 401 " pdb=" C39 L9Q A 401 " pdb=" C40 L9Q A 401 " ideal model delta sigma weight residual 127.57 110.38 17.19 3.00e+00 1.11e-01 3.28e+01 angle pdb=" C38 L9Q B 401 " pdb=" C39 L9Q B 401 " pdb=" C40 L9Q B 401 " ideal model delta sigma weight residual 127.57 110.61 16.96 3.00e+00 1.11e-01 3.20e+01 angle pdb=" C39 L9Q B 401 " pdb=" C40 L9Q B 401 " pdb=" C41 L9Q B 401 " ideal model delta sigma weight residual 127.59 114.62 12.97 3.00e+00 1.11e-01 1.87e+01 angle pdb=" C39 L9Q A 401 " pdb=" C40 L9Q A 401 " pdb=" C41 L9Q A 401 " ideal model delta sigma weight residual 127.59 114.75 12.84 3.00e+00 1.11e-01 1.83e+01 angle pdb=" N THR A 170 " pdb=" CA THR A 170 " pdb=" C THR A 170 " ideal model delta sigma weight residual 111.02 116.24 -5.22 1.25e+00 6.40e-01 1.74e+01 ... (remaining 5577 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.42: 2187 35.42 - 70.85: 116 70.85 - 106.27: 11 106.27 - 141.69: 2 141.69 - 177.11: 4 Dihedral angle restraints: 2320 sinusoidal: 920 harmonic: 1400 Sorted by residual: dihedral pdb=" CB CYS A 34 " pdb=" SG CYS A 34 " pdb=" SG CYS B 36 " pdb=" CB CYS B 36 " ideal model delta sinusoidal sigma weight residual 93.00 50.49 42.51 1 1.00e+01 1.00e-02 2.52e+01 dihedral pdb=" CB CYS A 36 " pdb=" SG CYS A 36 " pdb=" SG CYS B 34 " pdb=" CB CYS B 34 " ideal model delta sinusoidal sigma weight residual 93.00 50.50 42.50 1 1.00e+01 1.00e-02 2.52e+01 dihedral pdb=" C23 L9Q B 401 " pdb=" C24 L9Q B 401 " pdb=" C25 L9Q B 401 " pdb=" C26 L9Q B 401 " ideal model delta sinusoidal sigma weight residual 179.70 -3.19 -177.11 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 2317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 416 0.038 - 0.076: 146 0.076 - 0.113: 38 0.113 - 0.151: 0 0.151 - 0.189: 6 Chirality restraints: 606 Sorted by residual: chirality pdb=" C2 L9Q B 401 " pdb=" C1 L9Q B 401 " pdb=" C3 L9Q B 401 " pdb=" O2 L9Q B 401 " both_signs ideal model delta sigma weight residual False 2.36 2.55 -0.19 2.00e-01 2.50e+01 8.94e-01 chirality pdb=" CA THR A 170 " pdb=" N THR A 170 " pdb=" C THR A 170 " pdb=" CB THR A 170 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.71e-01 chirality pdb=" CA THR B 170 " pdb=" N THR B 170 " pdb=" C THR B 170 " pdb=" CB THR B 170 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.71e-01 ... (remaining 603 not shown) Planarity restraints: 666 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C38 L9Q B 401 " -0.208 2.00e-02 2.50e+03 2.16e-01 4.66e+02 pdb=" C39 L9Q B 401 " 0.184 2.00e-02 2.50e+03 pdb=" C40 L9Q B 401 " 0.245 2.00e-02 2.50e+03 pdb=" C41 L9Q B 401 " -0.221 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 L9Q A 401 " 0.205 2.00e-02 2.50e+03 2.13e-01 4.55e+02 pdb=" C39 L9Q A 401 " -0.180 2.00e-02 2.50e+03 pdb=" C40 L9Q A 401 " -0.244 2.00e-02 2.50e+03 pdb=" C41 L9Q A 401 " 0.219 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 203 " -0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO B 204 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 204 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 204 " -0.016 5.00e-02 4.00e+02 ... (remaining 663 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1028 2.79 - 3.32: 3977 3.32 - 3.85: 7431 3.85 - 4.37: 8711 4.37 - 4.90: 14518 Nonbonded interactions: 35665 Sorted by model distance: nonbonded pdb=" OG SER A 77 " pdb=" N THR A 78 " model vdw 2.265 3.120 nonbonded pdb=" OG SER B 77 " pdb=" N THR B 78 " model vdw 2.265 3.120 nonbonded pdb=" O TYR A 70 " pdb=" OG1 THR A 74 " model vdw 2.270 3.040 nonbonded pdb=" O TYR B 70 " pdb=" OG1 THR B 74 " model vdw 2.270 3.040 nonbonded pdb=" O ALA A 59 " pdb=" OG SER A 63 " model vdw 2.335 3.040 ... (remaining 35660 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 17.040 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: 0.310 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 20.280 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 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 0.190 4120 Z= 0.492 Angle : 0.868 17.187 5582 Z= 0.402 Chirality : 0.042 0.189 606 Planarity : 0.012 0.216 666 Dihedral : 22.820 177.109 1430 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.46 % Allowed : 26.11 % Favored : 71.43 % 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: 1.70 (0.38), residues: 488 helix: 2.06 (0.26), residues: 378 sheet: None (None), residues: 0 loop : -2.34 (0.57), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 118 HIS 0.003 0.001 HIS B 201 PHE 0.012 0.001 PHE B 177 TYR 0.010 0.001 TYR B 85 ARG 0.001 0.000 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.386 Fit side-chains outliers start: 10 outliers final: 10 residues processed: 52 average time/residue: 0.8647 time to fit residues: 47.2312 Evaluate side-chains 50 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 203 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.125841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.107583 restraints weight = 4217.074| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.58 r_work: 0.3107 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.0668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4120 Z= 0.215 Angle : 0.548 6.232 5582 Z= 0.290 Chirality : 0.041 0.148 606 Planarity : 0.003 0.022 666 Dihedral : 17.117 131.237 632 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.93 % Allowed : 19.70 % Favored : 75.37 % 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: 1.78 (0.38), residues: 488 helix: 1.95 (0.25), residues: 388 sheet: None (None), residues: 0 loop : -1.97 (0.62), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 118 HIS 0.004 0.001 HIS A 201 PHE 0.011 0.001 PHE B 177 TYR 0.012 0.001 TYR A 109 ARG 0.002 0.000 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 40 time to evaluate : 0.359 Fit side-chains outliers start: 20 outliers final: 10 residues processed: 60 average time/residue: 1.0069 time to fit residues: 63.0370 Evaluate side-chains 50 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 203 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 137 ASN A 201 HIS B 104 ASN B 137 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.126310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.107933 restraints weight = 4234.230| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.59 r_work: 0.3113 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4120 Z= 0.202 Angle : 0.545 9.791 5582 Z= 0.282 Chirality : 0.040 0.144 606 Planarity : 0.003 0.023 666 Dihedral : 14.515 112.578 628 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.69 % Allowed : 20.94 % Favored : 75.37 % 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: 1.87 (0.38), residues: 488 helix: 2.00 (0.25), residues: 388 sheet: None (None), residues: 0 loop : -1.90 (0.61), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 118 HIS 0.004 0.001 HIS A 201 PHE 0.010 0.001 PHE A 177 TYR 0.012 0.001 TYR B 109 ARG 0.002 0.000 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.435 Fit side-chains REVERT: A 104 ASN cc_start: 0.7331 (OUTLIER) cc_final: 0.7128 (t0) REVERT: B 194 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7284 (mttt) outliers start: 15 outliers final: 8 residues processed: 57 average time/residue: 0.9083 time to fit residues: 54.3285 Evaluate side-chains 48 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 257 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 137 ASN A 210 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 210 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.125459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.106989 restraints weight = 4264.142| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.60 r_work: 0.3097 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4120 Z= 0.218 Angle : 0.538 6.851 5582 Z= 0.284 Chirality : 0.040 0.151 606 Planarity : 0.003 0.022 666 Dihedral : 13.911 108.522 626 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.68 % Allowed : 19.46 % Favored : 75.86 % 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: 1.89 (0.38), residues: 488 helix: 2.01 (0.25), residues: 388 sheet: None (None), residues: 0 loop : -1.89 (0.61), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 118 HIS 0.004 0.001 HIS B 201 PHE 0.010 0.001 PHE A 177 TYR 0.012 0.001 TYR B 109 ARG 0.002 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 41 time to evaluate : 0.451 Fit side-chains REVERT: A 194 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7302 (mttt) REVERT: B 194 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7288 (mttt) outliers start: 19 outliers final: 10 residues processed: 60 average time/residue: 1.0123 time to fit residues: 63.3796 Evaluate side-chains 51 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 257 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 9 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 34 optimal weight: 0.0020 chunk 24 optimal weight: 0.0060 chunk 32 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 overall best weight: 0.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 210 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 210 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.128476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.110149 restraints weight = 4318.581| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.62 r_work: 0.3147 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4120 Z= 0.154 Angle : 0.522 10.858 5582 Z= 0.268 Chirality : 0.038 0.144 606 Planarity : 0.003 0.023 666 Dihedral : 13.258 99.870 626 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.69 % Allowed : 19.95 % Favored : 76.35 % 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: 2.16 (0.38), residues: 488 helix: 2.14 (0.25), residues: 390 sheet: None (None), residues: 0 loop : -1.57 (0.63), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 118 HIS 0.003 0.001 HIS B 201 PHE 0.007 0.001 PHE A 177 TYR 0.010 0.001 TYR A 109 ARG 0.001 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.438 Fit side-chains REVERT: A 194 LYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7288 (mttt) REVERT: B 194 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7283 (mttt) outliers start: 15 outliers final: 10 residues processed: 57 average time/residue: 0.9780 time to fit residues: 58.2685 Evaluate side-chains 48 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 257 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 46 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 210 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 210 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.124104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.105491 restraints weight = 4253.660| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.61 r_work: 0.3074 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4120 Z= 0.259 Angle : 0.570 9.221 5582 Z= 0.295 Chirality : 0.040 0.151 606 Planarity : 0.003 0.023 666 Dihedral : 13.200 97.859 626 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.93 % Allowed : 17.49 % Favored : 77.59 % 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: 1.91 (0.38), residues: 488 helix: 1.96 (0.25), residues: 390 sheet: None (None), residues: 0 loop : -1.68 (0.62), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 118 HIS 0.005 0.001 HIS B 201 PHE 0.011 0.002 PHE B 177 TYR 0.012 0.002 TYR A 109 ARG 0.001 0.000 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 43 time to evaluate : 0.410 Fit side-chains REVERT: A 194 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7334 (mttt) outliers start: 20 outliers final: 11 residues processed: 63 average time/residue: 0.8186 time to fit residues: 54.2201 Evaluate side-chains 53 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 257 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 10 optimal weight: 0.0770 chunk 12 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.127286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.108767 restraints weight = 4248.435| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.62 r_work: 0.3122 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4120 Z= 0.176 Angle : 0.512 7.665 5582 Z= 0.269 Chirality : 0.038 0.145 606 Planarity : 0.003 0.023 666 Dihedral : 12.216 89.871 626 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.94 % Allowed : 18.72 % Favored : 77.34 % 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: 2.09 (0.38), residues: 488 helix: 2.10 (0.25), residues: 390 sheet: None (None), residues: 0 loop : -1.63 (0.62), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 118 HIS 0.003 0.001 HIS B 201 PHE 0.008 0.001 PHE B 177 TYR 0.010 0.001 TYR A 109 ARG 0.001 0.000 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.423 Fit side-chains REVERT: A 194 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7329 (mttt) REVERT: B 194 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.7325 (mttt) outliers start: 16 outliers final: 10 residues processed: 58 average time/residue: 0.9757 time to fit residues: 59.1155 Evaluate side-chains 52 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 257 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 6 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 31 optimal weight: 0.0170 chunk 44 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 GLN B 104 ASN B 210 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.128093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.109568 restraints weight = 4211.120| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.61 r_work: 0.3127 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4120 Z= 0.172 Angle : 0.541 11.802 5582 Z= 0.273 Chirality : 0.038 0.144 606 Planarity : 0.003 0.023 666 Dihedral : 11.477 84.112 626 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.45 % Allowed : 19.46 % Favored : 77.09 % 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: 2.15 (0.38), residues: 488 helix: 2.15 (0.25), residues: 390 sheet: None (None), residues: 0 loop : -1.66 (0.62), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 118 HIS 0.003 0.001 HIS B 201 PHE 0.008 0.001 PHE B 177 TYR 0.010 0.001 TYR A 109 ARG 0.001 0.000 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.390 Fit side-chains REVERT: A 194 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7314 (mttt) REVERT: B 194 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7324 (mttt) outliers start: 14 outliers final: 6 residues processed: 55 average time/residue: 1.0406 time to fit residues: 59.6913 Evaluate side-chains 48 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 203 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 0.0170 chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 GLN B 210 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.128086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.109343 restraints weight = 4209.695| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.62 r_work: 0.3125 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4120 Z= 0.177 Angle : 0.534 10.791 5582 Z= 0.272 Chirality : 0.038 0.143 606 Planarity : 0.003 0.023 666 Dihedral : 11.040 76.253 626 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.97 % Allowed : 20.94 % Favored : 77.09 % 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: 2.14 (0.38), residues: 488 helix: 2.15 (0.25), residues: 390 sheet: None (None), residues: 0 loop : -1.71 (0.61), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 118 HIS 0.003 0.001 HIS B 201 PHE 0.008 0.001 PHE B 177 TYR 0.010 0.001 TYR A 109 ARG 0.001 0.000 ARG A 148 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.393 Fit side-chains REVERT: A 194 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7324 (mttt) REVERT: B 194 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.7330 (mttt) outliers start: 8 outliers final: 6 residues processed: 48 average time/residue: 0.9607 time to fit residues: 48.2617 Evaluate side-chains 47 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 203 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.123185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.104421 restraints weight = 4249.751| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.61 r_work: 0.3054 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4120 Z= 0.315 Angle : 0.611 11.154 5582 Z= 0.312 Chirality : 0.042 0.151 606 Planarity : 0.003 0.023 666 Dihedral : 11.550 64.377 626 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.71 % Allowed : 19.95 % Favored : 77.34 % 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: 1.81 (0.38), residues: 488 helix: 1.90 (0.25), residues: 390 sheet: None (None), residues: 0 loop : -1.71 (0.60), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 118 HIS 0.006 0.001 HIS B 201 PHE 0.014 0.002 PHE B 177 TYR 0.012 0.002 TYR B 121 ARG 0.001 0.000 ARG A 207 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.453 Fit side-chains REVERT: A 194 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7331 (mttt) REVERT: B 194 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.7331 (mttt) outliers start: 11 outliers final: 7 residues processed: 51 average time/residue: 0.8981 time to fit residues: 48.1376 Evaluate side-chains 49 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 203 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 46 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.0570 chunk 1 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 41 optimal weight: 0.0470 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN B 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.128627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.110108 restraints weight = 4175.243| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.61 r_work: 0.3141 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4120 Z= 0.152 Angle : 0.523 10.620 5582 Z= 0.268 Chirality : 0.038 0.141 606 Planarity : 0.003 0.023 666 Dihedral : 10.650 59.666 626 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.97 % Allowed : 20.69 % Favored : 77.34 % 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: 2.11 (0.38), residues: 488 helix: 2.12 (0.25), residues: 390 sheet: None (None), residues: 0 loop : -1.68 (0.61), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 118 HIS 0.002 0.001 HIS B 201 PHE 0.007 0.001 PHE B 177 TYR 0.009 0.001 TYR A 109 ARG 0.001 0.000 ARG A 207 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5397.01 seconds wall clock time: 94 minutes 37.06 seconds (5677.06 seconds total)