Starting phenix.real_space_refine on Fri May 9 13:06:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9as3_43803/05_2025/9as3_43803.cif Found real_map, /net/cci-nas-00/data/ceres_data/9as3_43803/05_2025/9as3_43803.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9as3_43803/05_2025/9as3_43803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9as3_43803/05_2025/9as3_43803.map" model { file = "/net/cci-nas-00/data/ceres_data/9as3_43803/05_2025/9as3_43803.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9as3_43803/05_2025/9as3_43803.cif" } resolution = 3.18 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= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 1278 2.51 5 N 286 2.21 5 O 311 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 1890 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1866 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 8, 'TRANS': 236} Chain breaks: 4 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 58 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'7LD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.12, per 1000 atoms: 1.12 Number of scatterers: 1890 At special positions: 0 Unit cell: (59.84, 70.4, 67.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 311 8.00 N 286 7.00 C 1278 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 227 " 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: 0.51 Conformation dependent library (CDL) restraints added in 299.4 milliseconds 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 470 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 0 sheets defined 82.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 84 through 99 removed outlier: 3.639A pdb=" N LEU A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET A 97 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 122 removed outlier: 3.805A pdb=" N LEU A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 147 through 179 Processing helix chain 'A' and resid 179 through 186 removed outlier: 3.824A pdb=" N PHE A 186 " --> pdb=" O HIS A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 207 removed outlier: 3.753A pdb=" N SER A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 removed outlier: 3.642A pdb=" N VAL A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.524A pdb=" N ILE A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 261 Processing helix chain 'A' and resid 316 through 347 Proline residue: A 338 - end of helix removed outlier: 3.863A pdb=" N VAL A 347 " --> pdb=" O ASN A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 382 removed outlier: 3.775A pdb=" N TRP A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA A 374 " --> pdb=" O TYR A 370 " (cutoff:3.500A) Proline residue: A 377 - end of helix removed outlier: 3.512A pdb=" N THR A 381 " --> pdb=" O PRO A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 393 132 hydrogen bonds defined for protein. 396 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.47 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 537 1.35 - 1.46: 506 1.46 - 1.58: 868 1.58 - 1.70: 0 1.70 - 1.82: 25 Bond restraints: 1936 Sorted by residual: bond pdb=" CA SER A 188 " pdb=" CB SER A 188 " ideal model delta sigma weight residual 1.528 1.492 0.036 1.34e-02 5.57e+03 7.31e+00 bond pdb=" N ASN A 384 " pdb=" CA ASN A 384 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.29e-02 6.01e+03 6.72e+00 bond pdb=" N ASN A 107 " pdb=" CA ASN A 107 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.31e-02 5.83e+03 6.63e+00 bond pdb=" N SER A 188 " pdb=" CA SER A 188 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.19e-02 7.06e+03 6.15e+00 bond pdb=" N TYR A 370 " pdb=" CA TYR A 370 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.71e+00 ... (remaining 1931 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 2384 1.24 - 2.48: 199 2.48 - 3.73: 39 3.73 - 4.97: 15 4.97 - 6.21: 8 Bond angle restraints: 2645 Sorted by residual: angle pdb=" CA PRO A 377 " pdb=" N PRO A 377 " pdb=" CD PRO A 377 " ideal model delta sigma weight residual 112.00 105.79 6.21 1.40e+00 5.10e-01 1.97e+01 angle pdb=" N PHE A 222 " pdb=" CA PHE A 222 " pdb=" C PHE A 222 " ideal model delta sigma weight residual 107.73 112.27 -4.54 1.34e+00 5.57e-01 1.15e+01 angle pdb=" CA ASN A 107 " pdb=" C ASN A 107 " pdb=" O ASN A 107 " ideal model delta sigma weight residual 121.81 118.91 2.90 1.18e+00 7.18e-01 6.05e+00 angle pdb=" CA SER A 188 " pdb=" C SER A 188 " pdb=" O SER A 188 " ideal model delta sigma weight residual 120.65 117.65 3.00 1.23e+00 6.61e-01 5.95e+00 angle pdb=" CA SER A 203 " pdb=" C SER A 203 " pdb=" O SER A 203 " ideal model delta sigma weight residual 120.82 118.31 2.51 1.05e+00 9.07e-01 5.71e+00 ... (remaining 2640 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.50: 1093 34.50 - 68.99: 29 68.99 - 103.49: 5 103.49 - 137.98: 0 137.98 - 172.48: 1 Dihedral angle restraints: 1128 sinusoidal: 409 harmonic: 719 Sorted by residual: dihedral pdb=" CA LYS A 223 " pdb=" C LYS A 223 " pdb=" N GLU A 224 " pdb=" CA GLU A 224 " ideal model delta harmonic sigma weight residual 180.00 155.79 24.21 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" C16 7LD A 501 " pdb=" C17 7LD A 501 " pdb=" N3 7LD A 501 " pdb=" C18 7LD A 501 " ideal model delta sinusoidal sigma weight residual 91.75 -95.77 -172.48 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" CA GLU A 224 " pdb=" C GLU A 224 " pdb=" N GLY A 225 " pdb=" CA GLY A 225 " ideal model delta harmonic sigma weight residual 180.00 -160.50 -19.50 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 1125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 260 0.052 - 0.103: 62 0.103 - 0.155: 7 0.155 - 0.207: 1 0.207 - 0.259: 1 Chirality restraints: 331 Sorted by residual: chirality pdb=" C11 7LD A 501 " pdb=" C15 7LD A 501 " pdb=" C9 7LD A 501 " pdb=" N2 7LD A 501 " both_signs ideal model delta sigma weight residual False 2.48 2.22 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA SER A 188 " pdb=" N SER A 188 " pdb=" C SER A 188 " pdb=" CB SER A 188 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.16e-01 chirality pdb=" CA VAL A 221 " pdb=" N VAL A 221 " pdb=" C VAL A 221 " pdb=" CB VAL A 221 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 328 not shown) Planarity restraints: 307 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 376 " 0.074 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO A 377 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO A 377 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 377 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 245 " -0.044 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO A 246 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 246 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 246 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 141 " 0.040 5.00e-02 4.00e+02 6.05e-02 5.86e+00 pdb=" N PRO A 142 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.035 5.00e-02 4.00e+02 ... (remaining 304 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 487 2.80 - 3.32: 1812 3.32 - 3.85: 3012 3.85 - 4.37: 3511 4.37 - 4.90: 5981 Nonbonded interactions: 14803 Sorted by model distance: nonbonded pdb=" O PRO A 377 " pdb=" OG1 THR A 381 " model vdw 2.269 3.040 nonbonded pdb=" O ALA A 161 " pdb=" ND1 HIS A 165 " model vdw 2.394 3.120 nonbonded pdb=" OD1 ASP A 155 " pdb=" N2 7LD A 501 " model vdw 2.400 3.120 nonbonded pdb=" OE1 GLN A 106 " pdb=" OH TYR A 111 " model vdw 2.446 3.040 nonbonded pdb=" OD2 ASP A 155 " pdb=" OH TYR A 370 " model vdw 2.456 3.040 ... (remaining 14798 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.370 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 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 : 0.006 0.060 1937 Z= 0.277 Angle : 0.859 6.212 2647 Z= 0.470 Chirality : 0.044 0.259 331 Planarity : 0.009 0.108 307 Dihedral : 18.431 172.476 655 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.50 % Allowed : 19.10 % Favored : 80.40 % 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: -2.31 (0.52), residues: 235 helix: -1.22 (0.35), residues: 194 sheet: None (None), residues: 0 loop : -2.10 (1.02), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 151 HIS 0.004 0.001 HIS A 182 PHE 0.007 0.001 PHE A 365 TYR 0.011 0.002 TYR A 153 ARG 0.001 0.000 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.27550 ( 132) hydrogen bonds : angle 8.56600 ( 396) SS BOND : bond 0.00212 ( 1) SS BOND : angle 0.27407 ( 2) covalent geometry : bond 0.00554 ( 1936) covalent geometry : angle 0.85941 ( 2645) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.202 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 36 average time/residue: 0.1318 time to fit residues: 5.6455 Evaluate side-chains 33 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 0.0470 chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.150121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.134977 restraints weight = 2419.433| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.46 r_work: 0.3409 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 1937 Z= 0.172 Angle : 0.590 4.982 2647 Z= 0.318 Chirality : 0.042 0.130 331 Planarity : 0.007 0.059 307 Dihedral : 13.567 170.014 275 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.51 % Allowed : 20.60 % Favored : 77.89 % 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: -0.20 (0.56), residues: 235 helix: 0.45 (0.37), residues: 203 sheet: None (None), residues: 0 loop : -3.46 (0.97), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 141 HIS 0.001 0.001 HIS A 165 PHE 0.011 0.001 PHE A 339 TYR 0.007 0.001 TYR A 370 ARG 0.001 0.000 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.04905 ( 132) hydrogen bonds : angle 4.50383 ( 396) SS BOND : bond 0.00294 ( 1) SS BOND : angle 0.39291 ( 2) covalent geometry : bond 0.00414 ( 1936) covalent geometry : angle 0.58973 ( 2645) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.205 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 32 average time/residue: 0.1063 time to fit residues: 4.1825 Evaluate side-chains 31 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 105 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 5 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 0.0770 chunk 10 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 15 optimal weight: 0.1980 chunk 0 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 chunk 8 optimal weight: 0.6980 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.149385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.134507 restraints weight = 2423.871| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.45 r_work: 0.3411 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1937 Z= 0.128 Angle : 0.537 5.372 2647 Z= 0.284 Chirality : 0.040 0.134 331 Planarity : 0.006 0.050 307 Dihedral : 12.799 164.211 275 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.01 % Allowed : 19.10 % Favored : 78.89 % 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: 0.74 (0.57), residues: 235 helix: 1.20 (0.38), residues: 200 sheet: None (None), residues: 0 loop : -3.66 (0.77), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 367 HIS 0.001 0.000 HIS A 183 PHE 0.008 0.001 PHE A 339 TYR 0.006 0.001 TYR A 370 ARG 0.001 0.000 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.03981 ( 132) hydrogen bonds : angle 3.92136 ( 396) SS BOND : bond 0.00207 ( 1) SS BOND : angle 0.32260 ( 2) covalent geometry : bond 0.00302 ( 1936) covalent geometry : angle 0.53674 ( 2645) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.202 Fit side-chains REVERT: A 132 MET cc_start: 0.7952 (tmm) cc_final: 0.7666 (tpp) REVERT: A 237 ILE cc_start: 0.7868 (tt) cc_final: 0.7571 (tt) outliers start: 4 outliers final: 4 residues processed: 33 average time/residue: 0.1141 time to fit residues: 4.6820 Evaluate side-chains 31 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 334 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 23 optimal weight: 0.3980 chunk 11 optimal weight: 0.8980 chunk 1 optimal weight: 0.0050 chunk 16 optimal weight: 0.2980 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 7 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 15 optimal weight: 0.4980 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.150991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.135966 restraints weight = 2401.837| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.39 r_work: 0.3419 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1937 Z= 0.119 Angle : 0.519 5.101 2647 Z= 0.273 Chirality : 0.040 0.152 331 Planarity : 0.005 0.050 307 Dihedral : 12.104 151.564 275 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.02 % Allowed : 19.10 % Favored : 77.89 % 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: 1.13 (0.58), residues: 235 helix: 1.51 (0.39), residues: 200 sheet: None (None), residues: 0 loop : -3.80 (0.70), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 367 HIS 0.001 0.000 HIS A 165 PHE 0.008 0.001 PHE A 243 TYR 0.006 0.001 TYR A 370 ARG 0.001 0.000 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.03621 ( 132) hydrogen bonds : angle 3.72670 ( 396) SS BOND : bond 0.00210 ( 1) SS BOND : angle 0.25263 ( 2) covalent geometry : bond 0.00278 ( 1936) covalent geometry : angle 0.51938 ( 2645) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.182 Fit side-chains REVERT: A 343 ASN cc_start: 0.7810 (t0) cc_final: 0.7568 (t0) outliers start: 6 outliers final: 5 residues processed: 30 average time/residue: 0.1120 time to fit residues: 4.1406 Evaluate side-chains 29 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 334 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 3 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 0.1980 chunk 23 optimal weight: 0.4980 chunk 7 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.149804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.134762 restraints weight = 2442.777| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.44 r_work: 0.3384 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1937 Z= 0.138 Angle : 0.543 5.641 2647 Z= 0.285 Chirality : 0.041 0.131 331 Planarity : 0.005 0.050 307 Dihedral : 11.499 132.106 275 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.02 % Allowed : 18.09 % Favored : 77.89 % 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: 1.06 (0.57), residues: 235 helix: 1.42 (0.39), residues: 201 sheet: None (None), residues: 0 loop : -3.68 (0.70), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 367 HIS 0.001 0.000 HIS A 165 PHE 0.009 0.001 PHE A 339 TYR 0.005 0.001 TYR A 153 ARG 0.001 0.000 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.03897 ( 132) hydrogen bonds : angle 3.71853 ( 396) SS BOND : bond 0.00275 ( 1) SS BOND : angle 0.29112 ( 2) covalent geometry : bond 0.00332 ( 1936) covalent geometry : angle 0.54336 ( 2645) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.201 Fit side-chains REVERT: A 343 ASN cc_start: 0.7752 (t0) cc_final: 0.7501 (t0) outliers start: 8 outliers final: 7 residues processed: 35 average time/residue: 0.1054 time to fit residues: 4.5556 Evaluate side-chains 36 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 334 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 16 optimal weight: 0.3980 chunk 20 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.142712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.127309 restraints weight = 2504.863| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.47 r_work: 0.3356 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1937 Z= 0.158 Angle : 0.570 6.377 2647 Z= 0.298 Chirality : 0.042 0.183 331 Planarity : 0.005 0.051 307 Dihedral : 11.543 127.658 275 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.02 % Allowed : 18.59 % Favored : 77.39 % 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: 0.97 (0.57), residues: 235 helix: 1.27 (0.38), residues: 206 sheet: None (None), residues: 0 loop : -3.84 (0.78), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 367 HIS 0.001 0.000 HIS A 165 PHE 0.010 0.001 PHE A 339 TYR 0.005 0.001 TYR A 380 ARG 0.001 0.000 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.04103 ( 132) hydrogen bonds : angle 3.79869 ( 396) SS BOND : bond 0.00366 ( 1) SS BOND : angle 0.33233 ( 2) covalent geometry : bond 0.00386 ( 1936) covalent geometry : angle 0.57056 ( 2645) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.190 Fit side-chains REVERT: A 132 MET cc_start: 0.7948 (tmm) cc_final: 0.7639 (tpp) REVERT: A 343 ASN cc_start: 0.7868 (t0) cc_final: 0.7596 (t0) outliers start: 8 outliers final: 7 residues processed: 37 average time/residue: 0.1006 time to fit residues: 4.6484 Evaluate side-chains 37 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 375 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 7 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 0.0070 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.3980 chunk 13 optimal weight: 3.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 = 0.3630 r_free = 0.3630 target = 0.143069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.127496 restraints weight = 2448.322| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.46 r_work: 0.3371 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 1937 Z= 0.145 Angle : 0.562 7.659 2647 Z= 0.292 Chirality : 0.042 0.186 331 Planarity : 0.005 0.051 307 Dihedral : 11.431 127.370 275 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.02 % Allowed : 19.10 % Favored : 76.88 % 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: 0.98 (0.57), residues: 235 helix: 1.36 (0.39), residues: 201 sheet: None (None), residues: 0 loop : -3.74 (0.69), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 367 HIS 0.001 0.000 HIS A 183 PHE 0.008 0.001 PHE A 339 TYR 0.006 0.001 TYR A 153 ARG 0.001 0.000 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.03887 ( 132) hydrogen bonds : angle 3.76037 ( 396) SS BOND : bond 0.00341 ( 1) SS BOND : angle 0.35506 ( 2) covalent geometry : bond 0.00351 ( 1936) covalent geometry : angle 0.56208 ( 2645) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.205 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 38 average time/residue: 0.1099 time to fit residues: 5.1588 Evaluate side-chains 38 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 375 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 5 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 0.0040 chunk 19 optimal weight: 0.5980 overall best weight: 0.4792 ------------------------------------------------------------------------------- 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 = 0.3753 r_free = 0.3753 target = 0.151556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.136978 restraints weight = 2464.869| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.42 r_work: 0.3375 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 1937 Z= 0.137 Angle : 0.557 8.218 2647 Z= 0.290 Chirality : 0.041 0.188 331 Planarity : 0.005 0.052 307 Dihedral : 11.371 126.812 275 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.02 % Allowed : 19.10 % Favored : 76.88 % 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: 1.09 (0.57), residues: 235 helix: 1.43 (0.39), residues: 201 sheet: None (None), residues: 0 loop : -3.64 (0.73), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 367 HIS 0.001 0.000 HIS A 165 PHE 0.008 0.001 PHE A 339 TYR 0.005 0.001 TYR A 153 ARG 0.001 0.000 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.03791 ( 132) hydrogen bonds : angle 3.72070 ( 396) SS BOND : bond 0.00315 ( 1) SS BOND : angle 0.35073 ( 2) covalent geometry : bond 0.00334 ( 1936) covalent geometry : angle 0.55717 ( 2645) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.185 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 36 average time/residue: 0.0983 time to fit residues: 4.3923 Evaluate side-chains 37 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 375 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 14 optimal weight: 0.1980 chunk 12 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 22 optimal weight: 0.0970 chunk 10 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 20 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.153381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.138382 restraints weight = 2487.407| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.47 r_work: 0.3387 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1937 Z= 0.126 Angle : 0.554 9.384 2647 Z= 0.286 Chirality : 0.041 0.188 331 Planarity : 0.005 0.051 307 Dihedral : 11.239 127.079 275 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.52 % Allowed : 20.10 % Favored : 76.38 % 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: 1.24 (0.58), residues: 235 helix: 1.52 (0.39), residues: 201 sheet: None (None), residues: 0 loop : -3.52 (0.76), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 367 HIS 0.001 0.000 HIS A 183 PHE 0.009 0.001 PHE A 243 TYR 0.004 0.001 TYR A 370 ARG 0.001 0.000 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.03575 ( 132) hydrogen bonds : angle 3.68676 ( 396) SS BOND : bond 0.00262 ( 1) SS BOND : angle 0.33239 ( 2) covalent geometry : bond 0.00301 ( 1936) covalent geometry : angle 0.55442 ( 2645) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.218 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 36 average time/residue: 0.1048 time to fit residues: 4.6765 Evaluate side-chains 36 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 334 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 0 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 1 optimal weight: 0.0980 chunk 14 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 23 optimal weight: 0.0870 chunk 3 optimal weight: 0.0670 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 overall best weight: 0.2496 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.156365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.141874 restraints weight = 2419.764| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.38 r_work: 0.3463 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1937 Z= 0.109 Angle : 0.532 9.451 2647 Z= 0.275 Chirality : 0.040 0.183 331 Planarity : 0.005 0.052 307 Dihedral : 10.945 129.378 275 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.52 % Allowed : 20.60 % Favored : 75.88 % 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: 1.58 (0.58), residues: 235 helix: 1.75 (0.39), residues: 201 sheet: None (None), residues: 0 loop : -3.43 (0.77), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 367 HIS 0.000 0.000 HIS A 165 PHE 0.009 0.001 PHE A 243 TYR 0.004 0.001 TYR A 370 ARG 0.001 0.000 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.03134 ( 132) hydrogen bonds : angle 3.57348 ( 396) SS BOND : bond 0.00142 ( 1) SS BOND : angle 0.27738 ( 2) covalent geometry : bond 0.00253 ( 1936) covalent geometry : angle 0.53195 ( 2645) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.200 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 32 average time/residue: 0.1146 time to fit residues: 4.5354 Evaluate side-chains 32 residues out of total 218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 334 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 15 optimal weight: 0.4980 chunk 7 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 4 optimal weight: 0.0270 overall best weight: 0.4238 ------------------------------------------------------------------------------- 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 = 0.3747 r_free = 0.3747 target = 0.151397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.136305 restraints weight = 2451.015| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.47 r_work: 0.3396 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1937 Z= 0.129 Angle : 0.555 8.299 2647 Z= 0.289 Chirality : 0.041 0.188 331 Planarity : 0.005 0.051 307 Dihedral : 11.143 127.960 275 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.52 % Allowed : 20.60 % Favored : 75.88 % 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: 1.46 (0.58), residues: 235 helix: 1.65 (0.38), residues: 201 sheet: None (None), residues: 0 loop : -3.29 (0.83), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 367 HIS 0.001 0.000 HIS A 165 PHE 0.009 0.001 PHE A 243 TYR 0.005 0.001 TYR A 370 ARG 0.001 0.000 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.03547 ( 132) hydrogen bonds : angle 3.62570 ( 396) SS BOND : bond 0.00284 ( 1) SS BOND : angle 0.25022 ( 2) covalent geometry : bond 0.00312 ( 1936) covalent geometry : angle 0.55473 ( 2645) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1445.88 seconds wall clock time: 26 minutes 5.28 seconds (1565.28 seconds total)