Starting phenix.real_space_refine on Wed Jul 23 11:51:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u5a_63867/07_2025/9u5a_63867_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u5a_63867/07_2025/9u5a_63867.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9u5a_63867/07_2025/9u5a_63867.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u5a_63867/07_2025/9u5a_63867.map" model { file = "/net/cci-nas-00/data/ceres_data/9u5a_63867/07_2025/9u5a_63867_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u5a_63867/07_2025/9u5a_63867_trim.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.090 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 26 5.16 5 C 2149 2.51 5 N 537 2.21 5 O 556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 3268 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3243 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 54 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'ZWY': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.52, per 1000 atoms: 2.61 Number of scatterers: 3268 At special positions: 0 Unit cell: (88.54, 58.716, 77.356, 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 26 16.00 O 556 8.00 N 537 7.00 C 2149 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 113 " distance=2.03 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS A 136 " distance=2.04 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: 2.01 Conformation dependent library (CDL) restraints added in 1.3 seconds 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 800 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 1 sheets defined 83.8% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 Processing helix chain 'A' and resid 17 through 36 removed outlier: 3.678A pdb=" N LEU A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Proline residue: A 27 - end of helix Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 37 through 40 Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 68 through 74 Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 127 through 132 Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 140 through 165 removed outlier: 4.216A pdb=" N TYR A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 187 Processing helix chain 'A' and resid 188 through 190 No H-bonds generated for 'chain 'A' and resid 188 through 190' Processing helix chain 'A' and resid 192 through 221 removed outlier: 3.544A pdb=" N GLY A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 252 removed outlier: 4.189A pdb=" N ALA A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL A 229 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY A 246 " --> pdb=" O GLN A 242 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 264 Processing helix chain 'A' and resid 264 through 272 removed outlier: 4.178A pdb=" N ALA A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 287 Processing helix chain 'A' and resid 288 through 302 Processing helix chain 'A' and resid 346 through 365 removed outlier: 4.099A pdb=" N GLY A 362 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 373 through 399 removed outlier: 3.511A pdb=" N LEU A 377 " --> pdb=" O ASP A 373 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A 394 " --> pdb=" O ALA A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 422 removed outlier: 3.683A pdb=" N GLN A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 454 Processing helix chain 'A' and resid 464 through 478 Processing helix chain 'A' and resid 478 through 483 removed outlier: 3.674A pdb=" N ILE A 482 " --> pdb=" O MET A 478 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 483 " --> pdb=" O GLY A 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 478 through 483' Processing helix chain 'A' and resid 484 through 487 removed outlier: 3.872A pdb=" N GLN A 487 " --> pdb=" O MET A 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 484 through 487' Processing helix chain 'A' and resid 491 through 512 Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 88 241 hydrogen bonds defined for protein. 714 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.35 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 485 1.32 - 1.44: 920 1.44 - 1.56: 1898 1.56 - 1.68: 2 1.68 - 1.81: 39 Bond restraints: 3344 Sorted by residual: bond pdb=" O22 ZWY A 601 " pdb=" S21 ZWY A 601 " ideal model delta sigma weight residual 1.457 1.674 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C ILE A 74 " pdb=" N PRO A 75 " ideal model delta sigma weight residual 1.329 1.386 -0.057 1.18e-02 7.18e+03 2.29e+01 bond pdb=" C ILE A 404 " pdb=" O ILE A 404 " ideal model delta sigma weight residual 1.237 1.193 0.044 1.13e-02 7.83e+03 1.48e+01 bond pdb=" C LEU A 414 " pdb=" O LEU A 414 " ideal model delta sigma weight residual 1.237 1.193 0.044 1.17e-02 7.31e+03 1.38e+01 bond pdb=" C LEU A 377 " pdb=" O LEU A 377 " ideal model delta sigma weight residual 1.237 1.194 0.042 1.17e-02 7.31e+03 1.31e+01 ... (remaining 3339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 4254 2.36 - 4.71: 245 4.71 - 7.07: 47 7.07 - 9.42: 10 9.42 - 11.78: 4 Bond angle restraints: 4560 Sorted by residual: angle pdb=" C LEU A 492 " pdb=" N PRO A 493 " pdb=" CA PRO A 493 " ideal model delta sigma weight residual 120.38 111.82 8.56 1.03e+00 9.43e-01 6.90e+01 angle pdb=" N ASN A 39 " pdb=" CA ASN A 39 " pdb=" C ASN A 39 " ideal model delta sigma weight residual 113.23 104.41 8.82 1.24e+00 6.50e-01 5.06e+01 angle pdb=" N PRO A 75 " pdb=" CA PRO A 75 " pdb=" C PRO A 75 " ideal model delta sigma weight residual 110.70 118.92 -8.22 1.22e+00 6.72e-01 4.54e+01 angle pdb=" N TRP A 93 " pdb=" CA TRP A 93 " pdb=" C TRP A 93 " ideal model delta sigma weight residual 113.15 106.09 7.06 1.19e+00 7.06e-01 3.52e+01 angle pdb=" N ILE A 148 " pdb=" CA ILE A 148 " pdb=" C ILE A 148 " ideal model delta sigma weight residual 111.00 104.92 6.08 1.09e+00 8.42e-01 3.11e+01 ... (remaining 4555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.05: 1816 15.05 - 30.11: 144 30.11 - 45.16: 28 45.16 - 60.21: 3 60.21 - 75.26: 3 Dihedral angle restraints: 1994 sinusoidal: 762 harmonic: 1232 Sorted by residual: dihedral pdb=" C ARG A 401 " pdb=" N ARG A 401 " pdb=" CA ARG A 401 " pdb=" CB ARG A 401 " ideal model delta harmonic sigma weight residual -122.60 -137.04 14.44 0 2.50e+00 1.60e-01 3.33e+01 dihedral pdb=" CB CYS A 85 " pdb=" SG CYS A 85 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual -86.00 -129.52 43.52 1 1.00e+01 1.00e-02 2.64e+01 dihedral pdb=" N ARG A 401 " pdb=" C ARG A 401 " pdb=" CA ARG A 401 " pdb=" CB ARG A 401 " ideal model delta harmonic sigma weight residual 122.80 132.96 -10.16 0 2.50e+00 1.60e-01 1.65e+01 ... (remaining 1991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 457 0.109 - 0.217: 81 0.217 - 0.325: 10 0.325 - 0.434: 3 0.434 - 0.542: 1 Chirality restraints: 552 Sorted by residual: chirality pdb=" CA ARG A 401 " pdb=" N ARG A 401 " pdb=" C ARG A 401 " pdb=" CB ARG A 401 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.35e+00 chirality pdb=" CA TYR A 165 " pdb=" N TYR A 165 " pdb=" C TYR A 165 " pdb=" CB TYR A 165 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CA TYR A 361 " pdb=" N TYR A 361 " pdb=" C TYR A 361 " pdb=" CB TYR A 361 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.00e+00 ... (remaining 549 not shown) Planarity restraints: 552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 ZWY A 601 " -0.038 2.00e-02 2.50e+03 4.52e-02 2.56e+01 pdb=" C13 ZWY A 601 " 0.026 2.00e-02 2.50e+03 pdb=" C14 ZWY A 601 " 0.074 2.00e-02 2.50e+03 pdb=" C15 ZWY A 601 " -0.013 2.00e-02 2.50e+03 pdb=" C19 ZWY A 601 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 94 " -0.020 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C GLN A 94 " 0.068 2.00e-02 2.50e+03 pdb=" O GLN A 94 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU A 95 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 152 " -0.015 2.00e-02 2.50e+03 2.90e-02 8.42e+00 pdb=" C GLY A 152 " 0.050 2.00e-02 2.50e+03 pdb=" O GLY A 152 " -0.019 2.00e-02 2.50e+03 pdb=" N ILE A 153 " -0.017 2.00e-02 2.50e+03 ... (remaining 549 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 1330 2.89 - 3.39: 3406 3.39 - 3.89: 5643 3.89 - 4.40: 6670 4.40 - 4.90: 10430 Nonbonded interactions: 27479 Sorted by model distance: nonbonded pdb=" O GLU A 107 " pdb=" OG1 THR A 110 " model vdw 2.387 3.040 nonbonded pdb=" CE MET A 35 " pdb=" O22 ZWY A 601 " model vdw 2.499 3.460 nonbonded pdb=" N TRP A 93 " pdb=" N GLN A 94 " model vdw 2.513 2.560 nonbonded pdb=" N ASN A 39 " pdb=" N PHE A 40 " model vdw 2.515 2.560 nonbonded pdb=" N THR A 23 " pdb=" N PHE A 24 " model vdw 2.539 2.560 ... (remaining 27474 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: 117.810 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 27.300 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:105.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 250.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 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 : 0.010 0.217 3346 Z= 0.742 Angle : 1.345 11.776 4564 Z= 0.894 Chirality : 0.088 0.542 552 Planarity : 0.008 0.057 552 Dihedral : 11.092 75.265 1188 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Cbeta Deviations : 0.25 % 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: 0.38 (0.42), residues: 418 helix: 0.84 (0.30), residues: 322 sheet: -3.79 (1.08), residues: 10 loop : -1.21 (0.63), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 255 HIS 0.007 0.002 HIS A 47 PHE 0.023 0.002 PHE A 211 TYR 0.021 0.003 TYR A 165 ARG 0.005 0.001 ARG A 473 Details of bonding type rmsd hydrogen bonds : bond 0.20144 ( 241) hydrogen bonds : angle 7.27894 ( 714) SS BOND : bond 0.00444 ( 2) SS BOND : angle 3.15806 ( 4) covalent geometry : bond 0.01034 ( 3344) covalent geometry : angle 1.34262 ( 4560) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.816 Fit side-chains REVERT: A 285 ILE cc_start: 0.7761 (mt) cc_final: 0.7506 (mt) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 1.1592 time to fit residues: 83.3062 Evaluate side-chains 43 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 242 GLN A 405 GLN A 424 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.171016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.140020 restraints weight = 3803.525| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.11 r_work: 0.3494 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3346 Z= 0.153 Angle : 0.611 6.605 4564 Z= 0.306 Chirality : 0.039 0.115 552 Planarity : 0.006 0.044 552 Dihedral : 6.883 84.525 513 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.68 % Allowed : 9.82 % Favored : 87.50 % 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: 1.90 (0.43), residues: 418 helix: 1.80 (0.29), residues: 321 sheet: -4.34 (0.90), residues: 10 loop : 0.10 (0.74), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 175 HIS 0.004 0.001 HIS A 52 PHE 0.016 0.002 PHE A 24 TYR 0.017 0.002 TYR A 165 ARG 0.006 0.001 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.04625 ( 241) hydrogen bonds : angle 4.15639 ( 714) SS BOND : bond 0.00280 ( 2) SS BOND : angle 1.36605 ( 4) covalent geometry : bond 0.00347 ( 3344) covalent geometry : angle 0.61040 ( 4560) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.747 Fit side-chains REVERT: A 285 ILE cc_start: 0.7328 (mt) cc_final: 0.7095 (mt) outliers start: 9 outliers final: 1 residues processed: 57 average time/residue: 1.4626 time to fit residues: 86.8940 Evaluate side-chains 38 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 12 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 34 optimal weight: 0.0870 chunk 13 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.3926 r_free = 0.3926 target = 0.167271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.135985 restraints weight = 3837.178| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.13 r_work: 0.3444 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3346 Z= 0.136 Angle : 0.562 7.649 4564 Z= 0.275 Chirality : 0.037 0.120 552 Planarity : 0.005 0.045 552 Dihedral : 6.365 80.424 513 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.38 % Allowed : 11.90 % Favored : 85.71 % 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: 2.58 (0.44), residues: 418 helix: 2.25 (0.30), residues: 320 sheet: -4.34 (0.84), residues: 10 loop : 0.56 (0.78), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 255 HIS 0.001 0.000 HIS A 52 PHE 0.031 0.002 PHE A 24 TYR 0.014 0.002 TYR A 165 ARG 0.009 0.001 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.04035 ( 241) hydrogen bonds : angle 3.89922 ( 714) SS BOND : bond 0.00235 ( 2) SS BOND : angle 1.03265 ( 4) covalent geometry : bond 0.00319 ( 3344) covalent geometry : angle 0.56110 ( 4560) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.348 Fit side-chains REVERT: A 215 LEU cc_start: 0.6807 (OUTLIER) cc_final: 0.6573 (mp) outliers start: 8 outliers final: 2 residues processed: 49 average time/residue: 0.9184 time to fit residues: 47.6126 Evaluate side-chains 41 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 215 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 chunk 35 optimal weight: 3.9990 chunk 5 optimal weight: 0.0970 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 0.1980 overall best weight: 0.3778 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.167922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.136260 restraints weight = 3865.821| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.23 r_work: 0.3458 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3346 Z= 0.109 Angle : 0.515 6.788 4564 Z= 0.250 Chirality : 0.036 0.125 552 Planarity : 0.004 0.036 552 Dihedral : 6.311 84.659 513 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.98 % Allowed : 14.88 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.43), residues: 418 helix: 2.48 (0.29), residues: 320 sheet: -4.19 (0.94), residues: 10 loop : 0.67 (0.77), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 255 HIS 0.001 0.000 HIS A 52 PHE 0.013 0.001 PHE A 511 TYR 0.012 0.001 TYR A 165 ARG 0.007 0.000 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.03465 ( 241) hydrogen bonds : angle 3.73124 ( 714) SS BOND : bond 0.00190 ( 2) SS BOND : angle 0.80206 ( 4) covalent geometry : bond 0.00244 ( 3344) covalent geometry : angle 0.51490 ( 4560) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.358 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 49 average time/residue: 1.2095 time to fit residues: 61.9842 Evaluate side-chains 42 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 411 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 0 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.165876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.133935 restraints weight = 3922.854| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.27 r_work: 0.3428 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3346 Z= 0.138 Angle : 0.540 6.645 4564 Z= 0.261 Chirality : 0.037 0.117 552 Planarity : 0.005 0.046 552 Dihedral : 6.453 88.350 513 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.57 % Allowed : 16.07 % Favored : 80.36 % 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: 2.94 (0.43), residues: 418 helix: 2.42 (0.29), residues: 320 sheet: -4.19 (0.98), residues: 10 loop : 1.04 (0.79), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 255 HIS 0.001 0.001 HIS A 83 PHE 0.025 0.001 PHE A 24 TYR 0.012 0.001 TYR A 165 ARG 0.011 0.001 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.03793 ( 241) hydrogen bonds : angle 3.77381 ( 714) SS BOND : bond 0.00240 ( 2) SS BOND : angle 0.94378 ( 4) covalent geometry : bond 0.00337 ( 3344) covalent geometry : angle 0.53965 ( 4560) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.355 Fit side-chains REVERT: A 398 PHE cc_start: 0.6365 (OUTLIER) cc_final: 0.6040 (m-10) outliers start: 12 outliers final: 4 residues processed: 53 average time/residue: 0.9034 time to fit residues: 50.0451 Evaluate side-chains 49 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 398 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 1 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3901 r_free = 0.3901 target = 0.164771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.132842 restraints weight = 3989.294| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.27 r_work: 0.3420 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3346 Z= 0.139 Angle : 0.550 7.455 4564 Z= 0.261 Chirality : 0.037 0.118 552 Planarity : 0.004 0.041 552 Dihedral : 5.918 78.936 513 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.98 % Allowed : 17.26 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.03 (0.43), residues: 418 helix: 2.51 (0.29), residues: 320 sheet: -3.92 (1.01), residues: 10 loop : 0.97 (0.78), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 255 HIS 0.002 0.001 HIS A 83 PHE 0.016 0.001 PHE A 24 TYR 0.011 0.001 TYR A 165 ARG 0.010 0.001 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.03756 ( 241) hydrogen bonds : angle 3.69567 ( 714) SS BOND : bond 0.00313 ( 2) SS BOND : angle 1.06720 ( 4) covalent geometry : bond 0.00342 ( 3344) covalent geometry : angle 0.54978 ( 4560) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.282 Fit side-chains REVERT: A 398 PHE cc_start: 0.6354 (OUTLIER) cc_final: 0.6004 (m-10) outliers start: 10 outliers final: 5 residues processed: 52 average time/residue: 0.8411 time to fit residues: 45.5901 Evaluate side-chains 46 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 398 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 0 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 7 optimal weight: 0.2980 chunk 11 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 29 optimal weight: 0.0170 overall best weight: 0.4418 ------------------------------------------------------------------------------- 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 = 0.3923 r_free = 0.3923 target = 0.166643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.135531 restraints weight = 3886.655| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.23 r_work: 0.3448 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3346 Z= 0.114 Angle : 0.531 6.927 4564 Z= 0.252 Chirality : 0.035 0.119 552 Planarity : 0.005 0.057 552 Dihedral : 5.818 77.767 513 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.98 % Allowed : 17.86 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.26 (0.43), residues: 418 helix: 2.69 (0.29), residues: 320 sheet: -3.75 (1.10), residues: 10 loop : 0.95 (0.79), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 255 HIS 0.001 0.000 HIS A 47 PHE 0.009 0.001 PHE A 24 TYR 0.010 0.001 TYR A 165 ARG 0.013 0.001 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.03506 ( 241) hydrogen bonds : angle 3.65536 ( 714) SS BOND : bond 0.00219 ( 2) SS BOND : angle 0.82991 ( 4) covalent geometry : bond 0.00269 ( 3344) covalent geometry : angle 0.53048 ( 4560) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.371 Fit side-chains REVERT: A 398 PHE cc_start: 0.6370 (OUTLIER) cc_final: 0.6018 (m-10) outliers start: 10 outliers final: 4 residues processed: 50 average time/residue: 0.7626 time to fit residues: 40.0340 Evaluate side-chains 46 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 398 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 21 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3884 r_free = 0.3884 target = 0.163084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.131283 restraints weight = 3868.489| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.23 r_work: 0.3403 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3346 Z= 0.162 Angle : 0.574 7.299 4564 Z= 0.275 Chirality : 0.038 0.118 552 Planarity : 0.005 0.054 552 Dihedral : 5.702 74.042 513 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.08 % Allowed : 17.86 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.05 (0.43), residues: 418 helix: 2.50 (0.29), residues: 322 sheet: -3.63 (1.08), residues: 10 loop : 0.99 (0.81), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 255 HIS 0.002 0.001 HIS A 47 PHE 0.011 0.001 PHE A 211 TYR 0.011 0.002 TYR A 165 ARG 0.013 0.001 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.04042 ( 241) hydrogen bonds : angle 3.75821 ( 714) SS BOND : bond 0.00289 ( 2) SS BOND : angle 1.01224 ( 4) covalent geometry : bond 0.00406 ( 3344) covalent geometry : angle 0.57346 ( 4560) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.346 Fit side-chains REVERT: A 398 PHE cc_start: 0.6412 (OUTLIER) cc_final: 0.6041 (m-10) outliers start: 7 outliers final: 5 residues processed: 44 average time/residue: 0.7728 time to fit residues: 35.7080 Evaluate side-chains 46 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 398 PHE Chi-restraints excluded: chain A residue 496 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 3.9990 chunk 32 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 chunk 7 optimal weight: 0.0980 chunk 0 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 0.0770 chunk 31 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- 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 = 0.3930 r_free = 0.3930 target = 0.167580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.136268 restraints weight = 3900.012| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.25 r_work: 0.3446 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3346 Z= 0.111 Angle : 0.531 7.655 4564 Z= 0.253 Chirality : 0.036 0.122 552 Planarity : 0.004 0.050 552 Dihedral : 5.713 75.993 513 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.49 % Allowed : 19.94 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.28 (0.43), residues: 418 helix: 2.67 (0.29), residues: 322 sheet: -3.52 (1.09), residues: 10 loop : 1.00 (0.82), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 255 HIS 0.001 0.000 HIS A 83 PHE 0.009 0.001 PHE A 211 TYR 0.009 0.001 TYR A 165 ARG 0.011 0.000 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.03437 ( 241) hydrogen bonds : angle 3.68044 ( 714) SS BOND : bond 0.00203 ( 2) SS BOND : angle 0.74178 ( 4) covalent geometry : bond 0.00261 ( 3344) covalent geometry : angle 0.53040 ( 4560) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.323 Fit side-chains REVERT: A 86 ARG cc_start: 0.6700 (ptp-110) cc_final: 0.6494 (ptp-110) REVERT: A 398 PHE cc_start: 0.6392 (OUTLIER) cc_final: 0.6014 (m-10) outliers start: 5 outliers final: 4 residues processed: 45 average time/residue: 0.7998 time to fit residues: 37.6782 Evaluate side-chains 44 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 398 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 37 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 0.1980 chunk 0 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 10 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3923 r_free = 0.3923 target = 0.167230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.135664 restraints weight = 3825.707| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.22 r_work: 0.3425 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3346 Z= 0.128 Angle : 0.538 7.666 4564 Z= 0.258 Chirality : 0.036 0.118 552 Planarity : 0.004 0.050 552 Dihedral : 5.699 75.485 513 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.49 % Allowed : 20.54 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.23 (0.43), residues: 418 helix: 2.64 (0.29), residues: 322 sheet: -3.45 (1.14), residues: 10 loop : 0.98 (0.82), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 255 HIS 0.001 0.001 HIS A 83 PHE 0.011 0.001 PHE A 24 TYR 0.010 0.001 TYR A 165 ARG 0.012 0.001 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.03610 ( 241) hydrogen bonds : angle 3.71496 ( 714) SS BOND : bond 0.00216 ( 2) SS BOND : angle 0.80882 ( 4) covalent geometry : bond 0.00312 ( 3344) covalent geometry : angle 0.53817 ( 4560) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.359 Fit side-chains REVERT: A 398 PHE cc_start: 0.6451 (OUTLIER) cc_final: 0.6038 (m-10) outliers start: 5 outliers final: 4 residues processed: 42 average time/residue: 0.7885 time to fit residues: 34.7631 Evaluate side-chains 45 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 398 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 40 optimal weight: 0.0370 chunk 1 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.166898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.135514 restraints weight = 3877.434| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.16 r_work: 0.3437 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3346 Z= 0.127 Angle : 0.540 7.630 4564 Z= 0.259 Chirality : 0.036 0.120 552 Planarity : 0.004 0.051 552 Dihedral : 5.703 75.312 513 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.49 % Allowed : 20.24 % Favored : 78.27 % 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: 3.22 (0.43), residues: 418 helix: 2.63 (0.29), residues: 322 sheet: -3.25 (1.23), residues: 10 loop : 0.96 (0.82), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 255 HIS 0.001 0.001 HIS A 83 PHE 0.011 0.001 PHE A 24 TYR 0.009 0.001 TYR A 165 ARG 0.011 0.001 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.03613 ( 241) hydrogen bonds : angle 3.71458 ( 714) SS BOND : bond 0.00246 ( 2) SS BOND : angle 0.85657 ( 4) covalent geometry : bond 0.00310 ( 3344) covalent geometry : angle 0.53965 ( 4560) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3552.85 seconds wall clock time: 65 minutes 3.94 seconds (3903.94 seconds total)