Starting phenix.real_space_refine on Tue Feb 11 03:44:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zam_39880/02_2025/8zam_39880_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zam_39880/02_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_39880/02_2025/8zam_39880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zam_39880/02_2025/8zam_39880.map" model { file = "/net/cci-nas-00/data/ceres_data/8zam_39880/02_2025/8zam_39880_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zam_39880/02_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-5592/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: 7.50, per 1000 atoms: 1.88 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: 0.98 Conformation dependent library (CDL) restraints added in 445.4 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: 0.31 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: 1.06 Time building geometry restraints manager: 1.08 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: 14.450 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: 0.270 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 17.930 Find NCS groups from input model: 0.060 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:11.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.480 ------------------------------------------------------------------------------- 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 : 0.378 Fit side-chains outliers start: 10 outliers final: 10 residues processed: 52 average time/residue: 0.8908 time to fit residues: 48.6085 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 : 0.457 ------------------------------------------------------------------------------- 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 = 4217.065| |-----------------------------------------------------------------------------| 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: 0.8163 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 : 17.117 131.235 632 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 : 0.442 Fit side-chains outliers start: 20 outliers final: 10 residues processed: 60 average time/residue: 1.0489 time to fit residues: 65.7597 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 : 0.426 ------------------------------------------------------------------------------- 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: 0.0370 chunk 12 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.127345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.109125 restraints weight = 4236.606| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.58 r_work: 0.3130 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.0894 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= 0.179 Angle : 0.529 9.518 5582 Z= 0.275 Chirality : 0.039 0.142 606 Planarity : 0.003 0.023 666 Dihedral : 14.426 111.493 628 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.69 % Allowed : 20.69 % Favored : 75.62 % 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: 1.96 (0.38), residues: 488 helix: 2.06 (0.25), residues: 388 sheet: None (None), residues: 0 loop : -1.85 (0.62), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 118 HIS 0.003 0.001 HIS A 201 PHE 0.009 0.001 PHE A 177 TYR 0.011 0.001 TYR A 109 ARG 0.001 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 : 0.455 Fit side-chains REVERT: A 104 ASN cc_start: 0.7341 (OUTLIER) cc_final: 0.7135 (t0) REVERT: B 104 ASN cc_start: 0.7341 (OUTLIER) cc_final: 0.7137 (t0) REVERT: B 194 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7282 (mttt) outliers start: 15 outliers final: 8 residues processed: 57 average time/residue: 0.9711 time to fit residues: 58.0340 Evaluate side-chains 49 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 104 ASN 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: 0.6980 chunk 34 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 0.0970 chunk 3 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 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 = 0.3480 r_free = 0.3480 target = 0.127333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.109030 restraints weight = 4258.658| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.60 r_work: 0.3132 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4120 Z= 0.182 Angle : 0.514 6.717 5582 Z= 0.272 Chirality : 0.039 0.141 606 Planarity : 0.003 0.022 666 Dihedral : 13.900 107.851 626 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.94 % Allowed : 20.20 % 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: 2.07 (0.38), residues: 488 helix: 2.14 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -1.82 (0.62), residues: 100 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 0.009 0.001 PHE A 177 TYR 0.011 0.001 TYR A 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 58 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.436 Fit side-chains REVERT: A 194 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7289 (mttt) REVERT: B 194 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7276 (mttt) outliers start: 16 outliers final: 8 residues processed: 58 average time/residue: 1.0571 time to fit residues: 63.8911 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 : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 1.9990 chunk 10 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 34 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 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 = 0.3459 r_free = 0.3459 target = 0.125742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.107131 restraints weight = 4334.917| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.62 r_work: 0.3102 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4120 Z= 0.213 Angle : 0.553 10.674 5582 Z= 0.284 Chirality : 0.040 0.142 606 Planarity : 0.003 0.023 666 Dihedral : 13.478 103.186 626 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.43 % Allowed : 19.21 % 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: 2.01 (0.38), residues: 488 helix: 2.09 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -1.80 (0.62), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 118 HIS 0.004 0.001 HIS B 201 PHE 0.010 0.001 PHE A 177 TYR 0.011 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 63 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 45 time to evaluate : 0.446 Fit side-chains REVERT: A 104 ASN cc_start: 0.7480 (OUTLIER) cc_final: 0.7224 (t0) REVERT: A 194 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7303 (mttt) REVERT: B 104 ASN cc_start: 0.7493 (OUTLIER) cc_final: 0.7235 (t0) REVERT: B 194 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7310 (mttt) outliers start: 18 outliers final: 10 residues processed: 63 average time/residue: 0.9497 time to fit residues: 62.6174 Evaluate side-chains 54 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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 104 ASN 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 104 ASN 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: 0.6980 chunk 42 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.126051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.107450 restraints weight = 4248.571| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.61 r_work: 0.3105 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4120 Z= 0.202 Angle : 0.532 8.849 5582 Z= 0.277 Chirality : 0.039 0.140 606 Planarity : 0.003 0.023 666 Dihedral : 12.728 94.079 626 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 5.17 % Allowed : 18.47 % 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: 2.05 (0.38), residues: 488 helix: 2.11 (0.25), residues: 388 sheet: None (None), residues: 0 loop : -1.77 (0.63), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 118 HIS 0.004 0.001 HIS B 201 PHE 0.009 0.001 PHE B 177 TYR 0.011 0.001 TYR B 109 ARG 0.001 0.000 ARG A 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: 21 poor density : 42 time to evaluate : 0.438 Fit side-chains REVERT: A 104 ASN cc_start: 0.7489 (OUTLIER) cc_final: 0.7243 (t0) REVERT: A 194 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7329 (mttt) REVERT: B 104 ASN cc_start: 0.7512 (OUTLIER) cc_final: 0.7264 (t0) outliers start: 21 outliers final: 14 residues processed: 63 average time/residue: 0.9176 time to fit residues: 60.4870 Evaluate side-chains 57 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 104 ASN Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 180 LEU 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 104 ASN Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 180 LEU 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: 0.0000 chunk 36 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3478 r_free = 0.3478 target = 0.127350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.108698 restraints weight = 4261.778| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.62 r_work: 0.3116 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1162 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= 0.175 Angle : 0.509 7.696 5582 Z= 0.267 Chirality : 0.038 0.138 606 Planarity : 0.003 0.023 666 Dihedral : 11.927 88.808 626 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.93 % Allowed : 17.98 % 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: 2.17 (0.38), residues: 488 helix: 2.20 (0.25), residues: 388 sheet: None (None), residues: 0 loop : -1.75 (0.63), residues: 100 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 0.008 0.001 PHE A 177 TYR 0.010 0.001 TYR A 109 ARG 0.001 0.000 ARG A 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: 20 poor density : 38 time to evaluate : 0.519 Fit side-chains REVERT: A 104 ASN cc_start: 0.7531 (OUTLIER) cc_final: 0.7315 (t0) REVERT: A 194 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7322 (mttt) REVERT: B 104 ASN cc_start: 0.7546 (OUTLIER) cc_final: 0.7329 (t0) REVERT: B 194 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7319 (mttt) outliers start: 20 outliers final: 11 residues processed: 58 average time/residue: 0.9613 time to fit residues: 58.2899 Evaluate side-chains 52 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 37 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 104 ASN Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 180 LEU 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 104 ASN Chi-restraints excluded: chain B residue 139 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 6 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 31 optimal weight: 0.4980 chunk 44 optimal weight: 0.1980 chunk 8 optimal weight: 0.0970 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 104 ASN A 210 GLN B 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.128607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.109922 restraints weight = 4213.317| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.63 r_work: 0.3137 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 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 0.023 4120 Z= 0.163 Angle : 0.535 11.569 5582 Z= 0.271 Chirality : 0.038 0.137 606 Planarity : 0.003 0.023 666 Dihedral : 11.164 82.158 626 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.43 % Allowed : 18.47 % 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: 2.23 (0.38), residues: 488 helix: 2.25 (0.25), residues: 388 sheet: None (None), residues: 0 loop : -1.75 (0.62), residues: 100 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 0.009 0.001 TYR A 109 ARG 0.001 0.000 ARG A 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 58 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 40 time to evaluate : 0.433 Fit side-chains REVERT: A 104 ASN cc_start: 0.7372 (OUTLIER) cc_final: 0.7145 (t0) REVERT: A 194 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7302 (mttt) REVERT: B 104 ASN cc_start: 0.7385 (OUTLIER) cc_final: 0.7146 (t0) REVERT: B 194 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7322 (mttt) outliers start: 18 outliers final: 7 residues processed: 58 average time/residue: 0.9084 time to fit residues: 55.2885 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 : 0.391 ------------------------------------------------------------------------------- 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 104 ASN 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 B residue 74 THR Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 104 ASN 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: 0.5980 chunk 20 optimal weight: 0.0970 chunk 4 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** 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 = 0.3486 r_free = 0.3486 target = 0.128187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.109535 restraints weight = 4222.900| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.63 r_work: 0.3128 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4120 Z= 0.178 Angle : 0.533 11.009 5582 Z= 0.271 Chirality : 0.039 0.138 606 Planarity : 0.003 0.023 666 Dihedral : 11.067 78.892 626 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.22 % Allowed : 21.18 % Favored : 76.60 % 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: 2.24 (0.38), residues: 488 helix: 2.21 (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 A 118 HIS 0.003 0.001 HIS B 201 PHE 0.008 0.001 PHE B 177 TYR 0.010 0.001 TYR B 109 ARG 0.001 0.000 ARG A 207 *********************** 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 49 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.441 Fit side-chains REVERT: A 194 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7307 (mttt) REVERT: B 194 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7328 (mttt) outliers start: 9 outliers final: 7 residues processed: 49 average time/residue: 0.9377 time to fit residues: 48.1635 Evaluate side-chains 48 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 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: 0.0060 chunk 2 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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 = 0.3469 r_free = 0.3469 target = 0.126784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.107911 restraints weight = 4241.895| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.63 r_work: 0.3109 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1252 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= 0.197 Angle : 0.549 10.964 5582 Z= 0.280 Chirality : 0.039 0.138 606 Planarity : 0.003 0.023 666 Dihedral : 10.938 70.204 626 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.50 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: 2.15 (0.38), residues: 488 helix: 2.15 (0.25), residues: 390 sheet: None (None), residues: 0 loop : -1.65 (0.62), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 118 HIS 0.004 0.001 HIS B 201 PHE 0.009 0.001 PHE B 177 TYR 0.010 0.001 TYR A 109 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 56 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.444 Fit side-chains REVERT: A 194 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7312 (mttt) REVERT: B 194 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7331 (mttt) outliers start: 15 outliers final: 7 residues processed: 56 average time/residue: 1.0861 time to fit residues: 63.6056 Evaluate side-chains 50 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 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 46 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.2980 chunk 1 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 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 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.126945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.108323 restraints weight = 4183.100| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.61 r_work: 0.3112 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1274 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= 0.198 Angle : 0.546 10.726 5582 Z= 0.280 Chirality : 0.039 0.144 606 Planarity : 0.003 0.023 666 Dihedral : 10.744 62.551 626 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.22 % Allowed : 21.43 % 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: 2.13 (0.38), residues: 488 helix: 2.13 (0.25), residues: 390 sheet: None (None), residues: 0 loop : -1.65 (0.62), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 118 HIS 0.004 0.001 HIS B 201 PHE 0.009 0.001 PHE B 177 TYR 0.010 0.001 TYR B 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: 4352.60 seconds wall clock time: 78 minutes 33.61 seconds (4713.61 seconds total)