Starting phenix.real_space_refine on Wed Jun 4 16:47:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hiq_34826/06_2025/8hiq_34826_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hiq_34826/06_2025/8hiq_34826.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hiq_34826/06_2025/8hiq_34826.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hiq_34826/06_2025/8hiq_34826.map" model { file = "/net/cci-nas-00/data/ceres_data/8hiq_34826/06_2025/8hiq_34826_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hiq_34826/06_2025/8hiq_34826_neut.cif" } resolution = 3.2 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= 0.001 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 3 5.49 5 S 14 5.16 5 C 2083 2.51 5 N 553 2.21 5 O 621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 3274 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3226 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 20, 'TRANS': 395} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.82, per 1000 atoms: 0.86 Number of scatterers: 3274 At special positions: 0 Unit cell: (68.034, 71.978, 71.978, 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 14 16.00 P 3 15.00 O 621 8.00 N 553 7.00 C 2083 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.87 Conformation dependent library (CDL) restraints added in 399.1 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 758 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 2 sheets defined 56.0% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 4 through 19 Processing helix chain 'A' and resid 24 through 33 Processing helix chain 'A' and resid 79 through 97 removed outlier: 4.059A pdb=" N VAL A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 149 through 165 Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.812A pdb=" N ILE A 174 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 207 Processing helix chain 'A' and resid 221 through 236 removed outlier: 3.686A pdb=" N GLY A 236 " --> pdb=" O LYS A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 280 through 286 removed outlier: 3.533A pdb=" N GLU A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 323 through 333 Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 344 through 361 removed outlier: 4.490A pdb=" N VAL A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 392 Processing helix chain 'A' and resid 394 through 415 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 45 removed outlier: 4.553A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N GLY A 71 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ILE A 108 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ARG A 73 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR A 68 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ALA A 143 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLY A 70 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 277 through 279 removed outlier: 7.479A pdb=" N ILE A 215 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL A 242 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL A 217 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LYS A 214 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ALA A 293 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA A 216 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU A 292 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL A 314 " --> pdb=" O ILE A 338 " (cutoff:3.500A) 184 hydrogen bonds defined for protein. 531 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: 0.90 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1062 1.34 - 1.46: 666 1.46 - 1.57: 1591 1.57 - 1.69: 5 1.69 - 1.81: 27 Bond restraints: 3351 Sorted by residual: bond pdb=" O2B NAP A 501 " pdb=" P2B NAP A 501 " ideal model delta sigma weight residual 1.736 1.614 0.122 2.00e-02 2.50e+03 3.69e+01 bond pdb=" C1D NAP A 501 " pdb=" O4D NAP A 501 " ideal model delta sigma weight residual 1.375 1.428 -0.053 2.00e-02 2.50e+03 7.04e+00 bond pdb=" C5D NAP A 501 " pdb=" O5D NAP A 501 " ideal model delta sigma weight residual 1.403 1.450 -0.047 2.00e-02 2.50e+03 5.54e+00 bond pdb=" O5D NAP A 501 " pdb=" PN NAP A 501 " ideal model delta sigma weight residual 1.649 1.604 0.045 2.00e-02 2.50e+03 5.05e+00 bond pdb=" O3 NAP A 501 " pdb=" PA NAP A 501 " ideal model delta sigma weight residual 1.647 1.604 0.043 2.00e-02 2.50e+03 4.53e+00 ... (remaining 3346 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 4403 1.76 - 3.52: 125 3.52 - 5.27: 25 5.27 - 7.03: 5 7.03 - 8.79: 3 Bond angle restraints: 4561 Sorted by residual: angle pdb=" CA MET A 153 " pdb=" CB MET A 153 " pdb=" CG MET A 153 " ideal model delta sigma weight residual 114.10 107.08 7.02 2.00e+00 2.50e-01 1.23e+01 angle pdb=" N GLY A 219 " pdb=" CA GLY A 219 " pdb=" C GLY A 219 " ideal model delta sigma weight residual 113.18 105.81 7.37 2.37e+00 1.78e-01 9.68e+00 angle pdb=" C VAL A 146 " pdb=" N TYR A 147 " pdb=" CA TYR A 147 " ideal model delta sigma weight residual 123.05 127.73 -4.68 1.57e+00 4.06e-01 8.89e+00 angle pdb=" N ARG A 166 " pdb=" CA ARG A 166 " pdb=" CB ARG A 166 " ideal model delta sigma weight residual 113.65 109.78 3.87 1.47e+00 4.63e-01 6.92e+00 angle pdb=" C2B NAP A 501 " pdb=" O2B NAP A 501 " pdb=" P2B NAP A 501 " ideal model delta sigma weight residual 117.19 109.33 7.86 3.00e+00 1.11e-01 6.87e+00 ... (remaining 4556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 1791 17.85 - 35.71: 175 35.71 - 53.56: 40 53.56 - 71.41: 19 71.41 - 89.27: 7 Dihedral angle restraints: 2032 sinusoidal: 843 harmonic: 1189 Sorted by residual: dihedral pdb=" CA TYR A 101 " pdb=" C TYR A 101 " pdb=" N GLY A 102 " pdb=" CA GLY A 102 " ideal model delta harmonic sigma weight residual 180.00 161.37 18.63 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CB GLU A 45 " pdb=" CG GLU A 45 " pdb=" CD GLU A 45 " pdb=" OE1 GLU A 45 " ideal model delta sinusoidal sigma weight residual 0.00 88.75 -88.75 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CA LYS A 213 " pdb=" C LYS A 213 " pdb=" N LYS A 214 " pdb=" CA LYS A 214 " ideal model delta harmonic sigma weight residual 180.00 -163.96 -16.04 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 2029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 267 0.025 - 0.050: 126 0.050 - 0.075: 55 0.075 - 0.099: 30 0.099 - 0.124: 23 Chirality restraints: 501 Sorted by residual: chirality pdb=" CA ILE A 108 " pdb=" N ILE A 108 " pdb=" C ILE A 108 " pdb=" CB ILE A 108 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA ILE A 338 " pdb=" N ILE A 338 " pdb=" C ILE A 338 " pdb=" CB ILE A 338 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.71e-01 chirality pdb=" CA ILE A 174 " pdb=" N ILE A 174 " pdb=" C ILE A 174 " pdb=" CB ILE A 174 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.68e-01 ... (remaining 498 not shown) Planarity restraints: 579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAP A 501 " -0.021 2.00e-02 2.50e+03 7.61e-02 1.16e+02 pdb=" C2N NAP A 501 " -0.071 2.00e-02 2.50e+03 pdb=" C3N NAP A 501 " -0.033 2.00e-02 2.50e+03 pdb=" C4N NAP A 501 " -0.125 2.00e-02 2.50e+03 pdb=" C5N NAP A 501 " 0.023 2.00e-02 2.50e+03 pdb=" C6N NAP A 501 " 0.108 2.00e-02 2.50e+03 pdb=" C7N NAP A 501 " 0.109 2.00e-02 2.50e+03 pdb=" N1N NAP A 501 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 141 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.17e+00 pdb=" N PRO A 142 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 323 " -0.026 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO A 324 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 324 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 324 " -0.022 5.00e-02 4.00e+02 ... (remaining 576 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 889 2.81 - 3.33: 3394 3.33 - 3.85: 5887 3.85 - 4.38: 6769 4.38 - 4.90: 11289 Nonbonded interactions: 28228 Sorted by model distance: nonbonded pdb=" OG1 THR A 68 " pdb=" OD1 ASP A 140 " model vdw 2.284 3.040 nonbonded pdb=" NZ LYS A 177 " pdb=" OD1 ASN A 358 " model vdw 2.300 3.120 nonbonded pdb=" O ASN A 308 " pdb=" NZ LYS A 310 " model vdw 2.319 3.120 nonbonded pdb=" OD1 ASN A 319 " pdb=" ND2 ASN A 344 " model vdw 2.320 3.120 nonbonded pdb=" NE2 GLN A 60 " pdb=" O VAL A 134 " model vdw 2.328 3.120 ... (remaining 28223 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.850 Find NCS groups from input model: 0.030 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: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 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 : 0.005 0.122 3351 Z= 0.234 Angle : 0.739 8.787 4561 Z= 0.405 Chirality : 0.043 0.124 501 Planarity : 0.006 0.076 579 Dihedral : 17.055 89.266 1274 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.43), residues: 414 helix: 1.97 (0.36), residues: 209 sheet: -0.06 (0.62), residues: 70 loop : 0.19 (0.58), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 89 HIS 0.002 0.001 HIS A 388 PHE 0.009 0.001 PHE A 341 TYR 0.010 0.001 TYR A 363 ARG 0.007 0.001 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.11605 ( 184) hydrogen bonds : angle 5.08940 ( 531) covalent geometry : bond 0.00470 ( 3351) covalent geometry : angle 0.73923 ( 4561) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.372 Fit side-chains REVERT: A 166 ARG cc_start: 0.5204 (ttt-90) cc_final: 0.4757 (ttt-90) REVERT: A 388 HIS cc_start: 0.6928 (t70) cc_final: 0.6714 (t-170) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.2358 time to fit residues: 17.0429 Evaluate side-chains 52 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN A 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.155933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.131347 restraints weight = 7087.582| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.76 r_work: 0.3672 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 3351 Z= 0.168 Angle : 0.553 7.376 4561 Z= 0.287 Chirality : 0.043 0.142 501 Planarity : 0.005 0.049 579 Dihedral : 10.494 59.450 517 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.61 % Allowed : 5.76 % Favored : 93.64 % 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: 1.41 (0.42), residues: 414 helix: 2.00 (0.35), residues: 213 sheet: 0.01 (0.69), residues: 60 loop : -0.22 (0.55), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.003 0.001 HIS A 388 PHE 0.009 0.001 PHE A 341 TYR 0.008 0.001 TYR A 408 ARG 0.005 0.001 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.04000 ( 184) hydrogen bonds : angle 4.47128 ( 531) covalent geometry : bond 0.00403 ( 3351) covalent geometry : angle 0.55349 ( 4561) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.362 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 56 average time/residue: 0.2198 time to fit residues: 14.3545 Evaluate side-chains 49 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 393 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 18 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.4146 r_free = 0.4146 target = 0.155525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.131199 restraints weight = 6958.309| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.70 r_work: 0.3673 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 3351 Z= 0.149 Angle : 0.522 7.556 4561 Z= 0.271 Chirality : 0.043 0.128 501 Planarity : 0.005 0.048 579 Dihedral : 9.430 57.630 517 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.52 % Allowed : 9.09 % Favored : 89.39 % 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: 1.41 (0.42), residues: 414 helix: 2.06 (0.35), residues: 213 sheet: -0.04 (0.69), residues: 60 loop : -0.32 (0.55), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 382 HIS 0.002 0.001 HIS A 388 PHE 0.009 0.001 PHE A 341 TYR 0.008 0.001 TYR A 408 ARG 0.003 0.000 ARG A 118 Details of bonding type rmsd hydrogen bonds : bond 0.03804 ( 184) hydrogen bonds : angle 4.40153 ( 531) covalent geometry : bond 0.00355 ( 3351) covalent geometry : angle 0.52244 ( 4561) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.328 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 56 average time/residue: 0.2176 time to fit residues: 14.2239 Evaluate side-chains 54 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 393 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4172 r_free = 0.4172 target = 0.157994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.133754 restraints weight = 7096.125| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.73 r_work: 0.3707 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3351 Z= 0.120 Angle : 0.496 7.135 4561 Z= 0.261 Chirality : 0.042 0.132 501 Planarity : 0.005 0.046 579 Dihedral : 8.783 59.045 517 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.21 % Allowed : 12.12 % Favored : 86.67 % 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: 1.40 (0.42), residues: 414 helix: 2.12 (0.35), residues: 213 sheet: 0.06 (0.69), residues: 60 loop : -0.49 (0.55), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.003 0.001 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.011 0.001 TYR A 250 ARG 0.006 0.000 ARG A 118 Details of bonding type rmsd hydrogen bonds : bond 0.03541 ( 184) hydrogen bonds : angle 4.27617 ( 531) covalent geometry : bond 0.00280 ( 3351) covalent geometry : angle 0.49646 ( 4561) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.399 Fit side-chains REVERT: A 111 ASN cc_start: 0.8728 (t0) cc_final: 0.8347 (t0) REVERT: A 166 ARG cc_start: 0.5899 (ttt-90) cc_final: 0.5462 (ttt-90) outliers start: 4 outliers final: 3 residues processed: 55 average time/residue: 0.2007 time to fit residues: 13.0515 Evaluate side-chains 52 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 393 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 32 optimal weight: 0.0770 overall best weight: 0.9940 ------------------------------------------------------------------------------- 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 = 0.4179 r_free = 0.4179 target = 0.158405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.133923 restraints weight = 7051.124| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.75 r_work: 0.3707 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3351 Z= 0.127 Angle : 0.522 6.967 4561 Z= 0.267 Chirality : 0.042 0.128 501 Planarity : 0.005 0.045 579 Dihedral : 8.396 56.926 517 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.82 % Allowed : 10.91 % Favored : 87.27 % 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: 1.42 (0.42), residues: 414 helix: 2.15 (0.35), residues: 213 sheet: 0.08 (0.70), residues: 60 loop : -0.51 (0.55), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 63 HIS 0.003 0.001 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.010 0.001 TYR A 250 ARG 0.007 0.001 ARG A 118 Details of bonding type rmsd hydrogen bonds : bond 0.03503 ( 184) hydrogen bonds : angle 4.24232 ( 531) covalent geometry : bond 0.00301 ( 3351) covalent geometry : angle 0.52194 ( 4561) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.368 Fit side-chains REVERT: A 111 ASN cc_start: 0.8737 (t0) cc_final: 0.8337 (t0) REVERT: A 377 MET cc_start: 0.6918 (mmt) cc_final: 0.6560 (mmt) outliers start: 6 outliers final: 6 residues processed: 56 average time/residue: 0.2200 time to fit residues: 14.4572 Evaluate side-chains 55 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 393 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 0.0870 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 = 0.4201 r_free = 0.4201 target = 0.160105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.135748 restraints weight = 7199.547| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.78 r_work: 0.3737 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3351 Z= 0.110 Angle : 0.505 6.603 4561 Z= 0.260 Chirality : 0.042 0.134 501 Planarity : 0.005 0.045 579 Dihedral : 8.057 55.064 517 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.21 % Allowed : 11.82 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.42), residues: 414 helix: 2.17 (0.35), residues: 214 sheet: 0.25 (0.71), residues: 60 loop : -0.51 (0.55), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.002 0.000 HIS A 388 PHE 0.008 0.001 PHE A 197 TYR 0.013 0.001 TYR A 20 ARG 0.006 0.000 ARG A 118 Details of bonding type rmsd hydrogen bonds : bond 0.03332 ( 184) hydrogen bonds : angle 4.13785 ( 531) covalent geometry : bond 0.00254 ( 3351) covalent geometry : angle 0.50491 ( 4561) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.336 Fit side-chains REVERT: A 111 ASN cc_start: 0.8703 (t0) cc_final: 0.8371 (t0) outliers start: 4 outliers final: 4 residues processed: 55 average time/residue: 0.2241 time to fit residues: 14.3951 Evaluate side-chains 52 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 277 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 24 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 17 optimal weight: 0.0670 chunk 14 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- 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 = 0.4204 r_free = 0.4204 target = 0.160308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.135997 restraints weight = 6966.388| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.73 r_work: 0.3743 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3351 Z= 0.115 Angle : 0.516 6.495 4561 Z= 0.265 Chirality : 0.042 0.127 501 Planarity : 0.005 0.046 579 Dihedral : 7.892 54.384 517 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.42 % Allowed : 13.94 % Favored : 83.64 % 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: 1.53 (0.42), residues: 414 helix: 2.18 (0.34), residues: 214 sheet: 0.37 (0.71), residues: 60 loop : -0.50 (0.55), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.003 0.001 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.016 0.001 TYR A 20 ARG 0.007 0.001 ARG A 118 Details of bonding type rmsd hydrogen bonds : bond 0.03320 ( 184) hydrogen bonds : angle 4.11191 ( 531) covalent geometry : bond 0.00271 ( 3351) covalent geometry : angle 0.51649 ( 4561) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.350 Fit side-chains REVERT: A 111 ASN cc_start: 0.8721 (t0) cc_final: 0.8397 (t0) REVERT: A 114 GLU cc_start: 0.7779 (pm20) cc_final: 0.7544 (pm20) REVERT: A 400 TYR cc_start: 0.8068 (OUTLIER) cc_final: 0.6389 (t80) outliers start: 8 outliers final: 5 residues processed: 58 average time/residue: 0.2174 time to fit residues: 14.8169 Evaluate side-chains 56 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 400 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 0.5980 chunk 2 optimal weight: 0.1980 chunk 16 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4216 r_free = 0.4216 target = 0.161377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.137093 restraints weight = 7094.182| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.78 r_work: 0.3756 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3351 Z= 0.113 Angle : 0.526 6.550 4561 Z= 0.270 Chirality : 0.042 0.128 501 Planarity : 0.005 0.045 579 Dihedral : 7.760 54.391 517 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.12 % Allowed : 14.85 % Favored : 83.03 % 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: 1.59 (0.42), residues: 414 helix: 2.18 (0.35), residues: 214 sheet: 0.49 (0.73), residues: 58 loop : -0.42 (0.55), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 63 HIS 0.002 0.001 HIS A 388 PHE 0.007 0.001 PHE A 341 TYR 0.016 0.001 TYR A 20 ARG 0.006 0.001 ARG A 118 Details of bonding type rmsd hydrogen bonds : bond 0.03304 ( 184) hydrogen bonds : angle 4.08076 ( 531) covalent geometry : bond 0.00267 ( 3351) covalent geometry : angle 0.52571 ( 4561) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.366 Fit side-chains REVERT: A 111 ASN cc_start: 0.8730 (t0) cc_final: 0.8346 (t0) REVERT: A 114 GLU cc_start: 0.7797 (pm20) cc_final: 0.7590 (pm20) REVERT: A 166 ARG cc_start: 0.5922 (ttt-90) cc_final: 0.5618 (ttt-90) REVERT: A 251 ASN cc_start: 0.8052 (t0) cc_final: 0.7523 (t0) REVERT: A 400 TYR cc_start: 0.8009 (OUTLIER) cc_final: 0.6608 (t80) outliers start: 7 outliers final: 5 residues processed: 61 average time/residue: 0.2161 time to fit residues: 15.5001 Evaluate side-chains 57 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 400 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 29 optimal weight: 8.9990 chunk 5 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 ASN A 360 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.161208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.136698 restraints weight = 7076.135| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.75 r_work: 0.3750 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3351 Z= 0.123 Angle : 0.540 6.553 4561 Z= 0.279 Chirality : 0.043 0.161 501 Planarity : 0.005 0.052 579 Dihedral : 7.710 54.931 517 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.12 % Allowed : 14.24 % Favored : 83.64 % 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 (0.43), residues: 414 helix: 2.28 (0.34), residues: 214 sheet: 0.49 (0.70), residues: 63 loop : -0.40 (0.57), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 63 HIS 0.003 0.001 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.021 0.001 TYR A 20 ARG 0.007 0.001 ARG A 118 Details of bonding type rmsd hydrogen bonds : bond 0.03373 ( 184) hydrogen bonds : angle 4.12386 ( 531) covalent geometry : bond 0.00294 ( 3351) covalent geometry : angle 0.53953 ( 4561) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.338 Fit side-chains REVERT: A 111 ASN cc_start: 0.8757 (t0) cc_final: 0.8332 (t0) REVERT: A 114 GLU cc_start: 0.7812 (pm20) cc_final: 0.7609 (pm20) REVERT: A 251 ASN cc_start: 0.8078 (t0) cc_final: 0.7523 (t0) REVERT: A 400 TYR cc_start: 0.8023 (OUTLIER) cc_final: 0.6353 (t80) outliers start: 7 outliers final: 5 residues processed: 59 average time/residue: 0.2186 time to fit residues: 15.1408 Evaluate side-chains 57 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 400 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 0.0050 chunk 39 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 22 optimal weight: 0.0010 chunk 25 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 overall best weight: 0.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.163034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.139099 restraints weight = 6943.184| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.72 r_work: 0.3778 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3351 Z= 0.112 Angle : 0.531 6.265 4561 Z= 0.277 Chirality : 0.042 0.163 501 Planarity : 0.005 0.054 579 Dihedral : 7.571 55.495 517 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.82 % Allowed : 14.24 % Favored : 83.94 % 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: 1.65 (0.43), residues: 414 helix: 2.28 (0.34), residues: 215 sheet: 0.48 (0.70), residues: 63 loop : -0.54 (0.56), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.002 0.001 HIS A 388 PHE 0.009 0.001 PHE A 197 TYR 0.008 0.001 TYR A 250 ARG 0.007 0.001 ARG A 118 Details of bonding type rmsd hydrogen bonds : bond 0.03324 ( 184) hydrogen bonds : angle 4.07002 ( 531) covalent geometry : bond 0.00260 ( 3351) covalent geometry : angle 0.53052 ( 4561) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.379 Fit side-chains REVERT: A 111 ASN cc_start: 0.8754 (t0) cc_final: 0.8329 (t0) REVERT: A 161 GLU cc_start: 0.8318 (tt0) cc_final: 0.8087 (tp30) REVERT: A 238 THR cc_start: 0.6431 (OUTLIER) cc_final: 0.6190 (t) REVERT: A 251 ASN cc_start: 0.8053 (t0) cc_final: 0.7519 (t0) REVERT: A 400 TYR cc_start: 0.7944 (OUTLIER) cc_final: 0.6580 (t80) outliers start: 6 outliers final: 3 residues processed: 61 average time/residue: 0.2159 time to fit residues: 15.4563 Evaluate side-chains 57 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 400 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 3.9990 chunk 17 optimal weight: 0.1980 chunk 35 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 281 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.162720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.138155 restraints weight = 6990.231| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.76 r_work: 0.3774 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3351 Z= 0.126 Angle : 0.576 6.862 4561 Z= 0.296 Chirality : 0.043 0.164 501 Planarity : 0.005 0.058 579 Dihedral : 7.556 55.461 517 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.21 % Allowed : 16.67 % Favored : 82.12 % 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 (0.43), residues: 414 helix: 2.35 (0.35), residues: 215 sheet: 0.50 (0.69), residues: 63 loop : -0.55 (0.56), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 30 HIS 0.003 0.001 HIS A 388 PHE 0.009 0.001 PHE A 197 TYR 0.027 0.001 TYR A 20 ARG 0.007 0.001 ARG A 118 Details of bonding type rmsd hydrogen bonds : bond 0.03402 ( 184) hydrogen bonds : angle 4.08255 ( 531) covalent geometry : bond 0.00304 ( 3351) covalent geometry : angle 0.57571 ( 4561) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2078.00 seconds wall clock time: 36 minutes 19.51 seconds (2179.51 seconds total)