Starting phenix.real_space_refine on Fri Aug 22 15:14:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hrn_34979/08_2025/8hrn_34979.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hrn_34979/08_2025/8hrn_34979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hrn_34979/08_2025/8hrn_34979.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hrn_34979/08_2025/8hrn_34979.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hrn_34979/08_2025/8hrn_34979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hrn_34979/08_2025/8hrn_34979.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.037 sd= 0.100 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 29 5.16 5 C 3115 2.51 5 N 806 2.21 5 O 920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4870 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Time building chain proxies: 1.15, per 1000 atoms: 0.24 Number of scatterers: 4870 At special positions: 0 Unit cell: (84.0942, 85.1324, 71.6358, 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 29 16.00 O 920 8.00 N 806 7.00 C 3115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " 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: 0.34 Conformation dependent library (CDL) restraints added in 153.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1130 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 3 sheets defined 65.5% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 20 through 34 Processing helix chain 'A' and resid 35 through 53 removed outlier: 3.588A pdb=" N GLN A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.779A pdb=" N GLN A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 removed outlier: 3.921A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 100 " --> pdb=" O GLN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.569A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.747A pdb=" N SER A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 154 removed outlier: 3.560A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 172 removed outlier: 3.964A pdb=" N ALA A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 193 removed outlier: 3.567A pdb=" N GLU A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 220 through 249 removed outlier: 3.887A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.756A pdb=" N MET A 249 " --> pdb=" O ARG A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 299 removed outlier: 4.227A pdb=" N VAL A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASP A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.954A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 4.003A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.792A pdb=" N ALA A 384 " --> pdb=" O GLN A 380 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 400 through 411 removed outlier: 3.718A pdb=" N VAL A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLU A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.648A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 465 removed outlier: 4.208A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 473 Processing helix chain 'A' and resid 474 through 482 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 4.686A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.896A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.611A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 removed outlier: 4.389A pdb=" N VAL A 132 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 142 " --> pdb=" O VAL A 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.452A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 5.500A pdb=" N ALA A 348 " --> pdb=" O LEU A 359 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU A 359 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ASP A 350 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ARG A 357 " --> pdb=" O ASP A 350 " (cutoff:3.500A) 225 hydrogen bonds defined for protein. 645 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: 0.71 Time building geometry restraints manager: 0.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1575 1.34 - 1.46: 1252 1.46 - 1.58: 2129 1.58 - 1.70: 1 1.70 - 1.82: 50 Bond restraints: 5007 Sorted by residual: bond pdb=" CB PRO A 565 " pdb=" CG PRO A 565 " ideal model delta sigma weight residual 1.492 1.655 -0.163 5.00e-02 4.00e+02 1.06e+01 bond pdb=" CG PRO A 565 " pdb=" CD PRO A 565 " ideal model delta sigma weight residual 1.503 1.412 0.091 3.40e-02 8.65e+02 7.12e+00 bond pdb=" N PRO A 565 " pdb=" CD PRO A 565 " ideal model delta sigma weight residual 1.473 1.507 -0.034 1.40e-02 5.10e+03 5.88e+00 bond pdb=" N PRO A 565 " pdb=" CA PRO A 565 " ideal model delta sigma weight residual 1.465 1.442 0.023 1.10e-02 8.26e+03 4.23e+00 bond pdb=" CG LEU A 595 " pdb=" CD1 LEU A 595 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.59e+00 ... (remaining 5002 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 6728 3.36 - 6.73: 66 6.73 - 10.09: 8 10.09 - 13.46: 0 13.46 - 16.82: 1 Bond angle restraints: 6803 Sorted by residual: angle pdb=" CA PRO A 565 " pdb=" N PRO A 565 " pdb=" CD PRO A 565 " ideal model delta sigma weight residual 112.00 95.18 16.82 1.40e+00 5.10e-01 1.44e+02 angle pdb=" N PRO A 565 " pdb=" CD PRO A 565 " pdb=" CG PRO A 565 " ideal model delta sigma weight residual 103.20 95.37 7.83 1.50e+00 4.44e-01 2.72e+01 angle pdb=" C LEU A 267 " pdb=" N GLY A 268 " pdb=" CA GLY A 268 " ideal model delta sigma weight residual 123.30 119.20 4.10 1.06e+00 8.90e-01 1.49e+01 angle pdb=" CB LYS A 476 " pdb=" CG LYS A 476 " pdb=" CD LYS A 476 " ideal model delta sigma weight residual 111.30 119.28 -7.98 2.30e+00 1.89e-01 1.20e+01 angle pdb=" CA PRO A 565 " pdb=" CB PRO A 565 " pdb=" CG PRO A 565 " ideal model delta sigma weight residual 104.50 98.19 6.31 1.90e+00 2.77e-01 1.10e+01 ... (remaining 6798 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 2518 17.90 - 35.80: 349 35.80 - 53.70: 70 53.70 - 71.59: 17 71.59 - 89.49: 5 Dihedral angle restraints: 2959 sinusoidal: 1205 harmonic: 1754 Sorted by residual: dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual 93.00 49.70 43.30 1 1.00e+01 1.00e-02 2.61e+01 dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 135.56 -42.56 1 1.00e+01 1.00e-02 2.53e+01 dihedral pdb=" CA CYS A 530 " pdb=" C CYS A 530 " pdb=" N GLN A 531 " pdb=" CA GLN A 531 " ideal model delta harmonic sigma weight residual 180.00 160.07 19.93 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 2956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 548 0.056 - 0.112: 145 0.112 - 0.167: 13 0.167 - 0.223: 3 0.223 - 0.279: 1 Chirality restraints: 710 Sorted by residual: chirality pdb=" CB VAL A 293 " pdb=" CA VAL A 293 " pdb=" CG1 VAL A 293 " pdb=" CG2 VAL A 293 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA PRO A 565 " pdb=" N PRO A 565 " pdb=" C PRO A 565 " pdb=" CB PRO A 565 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ASP A 206 " pdb=" N ASP A 206 " pdb=" C ASP A 206 " pdb=" CB ASP A 206 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.75e-01 ... (remaining 707 not shown) Planarity restraints: 881 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 564 " 0.099 5.00e-02 4.00e+02 1.35e-01 2.93e+01 pdb=" N PRO A 565 " -0.233 5.00e-02 4.00e+02 pdb=" CA PRO A 565 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 565 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 137 " -0.043 5.00e-02 4.00e+02 6.59e-02 6.94e+00 pdb=" N PRO A 138 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 138 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 138 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 478 " 0.003 2.00e-02 2.50e+03 1.32e-02 4.35e+00 pdb=" CG TRP A 478 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP A 478 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A 478 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 478 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 478 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 478 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 478 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 478 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A 478 " -0.007 2.00e-02 2.50e+03 ... (remaining 878 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 89 2.64 - 3.21: 4883 3.21 - 3.77: 8361 3.77 - 4.34: 11050 4.34 - 4.90: 17182 Nonbonded interactions: 41565 Sorted by model distance: nonbonded pdb=" OH TYR A 217 " pdb=" OD2 ASP A 225 " model vdw 2.080 3.040 nonbonded pdb=" NE2 GLN A 81 " pdb=" OD1 ASN A 103 " model vdw 2.150 3.120 nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.151 3.040 nonbonded pdb=" O LEU A 333 " pdb=" OG1 THR A 362 " model vdw 2.176 3.040 nonbonded pdb=" NH1 ARG A 177 " pdb=" O GLU A 495 " model vdw 2.198 3.120 ... (remaining 41560 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 group one per residue 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: 0.150 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.540 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 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 0.163 5010 Z= 0.227 Angle : 0.912 16.822 6809 Z= 0.532 Chirality : 0.050 0.279 710 Planarity : 0.007 0.135 881 Dihedral : 17.072 89.492 1820 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 24.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.95 % Allowed : 21.44 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.35), residues: 595 helix: -0.62 (0.28), residues: 347 sheet: -1.41 (1.34), residues: 12 loop : -0.71 (0.43), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 169 TYR 0.027 0.002 TYR A 385 PHE 0.020 0.002 PHE A 452 TRP 0.031 0.003 TRP A 478 HIS 0.006 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00508 ( 5007) covalent geometry : angle 0.91215 ( 6803) SS BOND : bond 0.00523 ( 3) SS BOND : angle 1.03335 ( 6) hydrogen bonds : bond 0.18856 ( 225) hydrogen bonds : angle 6.75314 ( 645) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7403 (tmm) cc_final: 0.6908 (tmm) REVERT: A 391 LEU cc_start: 0.6794 (mt) cc_final: 0.6566 (mp) REVERT: A 476 LYS cc_start: 0.8108 (mmmt) cc_final: 0.7146 (tppp) outliers start: 5 outliers final: 3 residues processed: 65 average time/residue: 0.0743 time to fit residues: 6.2599 Evaluate side-chains 61 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 597 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 2.9990 chunk 24 optimal weight: 30.0000 chunk 48 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 chunk 31 optimal weight: 20.0000 chunk 25 optimal weight: 0.0980 chunk 58 optimal weight: 30.0000 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.109056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.094069 restraints weight = 18540.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.096589 restraints weight = 11339.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.098051 restraints weight = 7903.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.099546 restraints weight = 6156.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.099951 restraints weight = 4952.004| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5010 Z= 0.174 Angle : 0.689 9.612 6809 Z= 0.351 Chirality : 0.045 0.233 710 Planarity : 0.005 0.061 881 Dihedral : 5.513 56.840 649 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.28 % Allowed : 20.11 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.35), residues: 595 helix: -0.26 (0.28), residues: 351 sheet: -1.41 (1.33), residues: 12 loop : -0.50 (0.45), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 518 TYR 0.011 0.002 TYR A 516 PHE 0.019 0.002 PHE A 452 TRP 0.015 0.002 TRP A 478 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 5007) covalent geometry : angle 0.68880 ( 6803) SS BOND : bond 0.00363 ( 3) SS BOND : angle 0.86312 ( 6) hydrogen bonds : bond 0.04607 ( 225) hydrogen bonds : angle 4.98461 ( 645) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7501 (tmm) cc_final: 0.6920 (tmm) REVERT: A 165 TRP cc_start: 0.3471 (t60) cc_final: 0.2767 (t60) REVERT: A 340 GLN cc_start: 0.7092 (OUTLIER) cc_final: 0.5880 (pp30) outliers start: 12 outliers final: 5 residues processed: 75 average time/residue: 0.0710 time to fit residues: 6.9329 Evaluate side-chains 64 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 545 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 7 optimal weight: 20.0000 chunk 53 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.110258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.095043 restraints weight = 18490.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.097638 restraints weight = 11274.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.099498 restraints weight = 7833.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.100500 restraints weight = 5975.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.101396 restraints weight = 4991.695| |-----------------------------------------------------------------------------| r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5010 Z= 0.140 Angle : 0.642 10.237 6809 Z= 0.320 Chirality : 0.042 0.133 710 Planarity : 0.005 0.046 881 Dihedral : 4.742 18.943 642 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.80 % Allowed : 19.17 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.36), residues: 595 helix: -0.23 (0.28), residues: 354 sheet: -1.48 (1.29), residues: 12 loop : -0.30 (0.45), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 518 TYR 0.032 0.002 TYR A 237 PHE 0.015 0.001 PHE A 452 TRP 0.012 0.001 TRP A 473 HIS 0.010 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 5007) covalent geometry : angle 0.64148 ( 6803) SS BOND : bond 0.00230 ( 3) SS BOND : angle 0.77224 ( 6) hydrogen bonds : bond 0.04173 ( 225) hydrogen bonds : angle 4.86204 ( 645) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7604 (tmm) cc_final: 0.6984 (tmm) REVERT: A 165 TRP cc_start: 0.3554 (t60) cc_final: 0.2858 (t60) REVERT: A 171 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7494 (pm20) REVERT: A 340 GLN cc_start: 0.6956 (OUTLIER) cc_final: 0.5872 (pp30) REVERT: A 376 MET cc_start: 0.5050 (tpp) cc_final: 0.4781 (mmm) outliers start: 20 outliers final: 6 residues processed: 82 average time/residue: 0.0648 time to fit residues: 7.0917 Evaluate side-chains 65 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 545 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 41 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 47 optimal weight: 20.0000 chunk 45 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 22 optimal weight: 30.0000 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.110531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.095381 restraints weight = 18431.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.097963 restraints weight = 11265.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.099622 restraints weight = 7816.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.100801 restraints weight = 6032.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.101834 restraints weight = 4910.026| |-----------------------------------------------------------------------------| r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5010 Z= 0.137 Angle : 0.642 12.281 6809 Z= 0.318 Chirality : 0.042 0.162 710 Planarity : 0.004 0.042 881 Dihedral : 4.617 17.313 642 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.85 % Allowed : 21.25 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.35), residues: 595 helix: -0.02 (0.28), residues: 345 sheet: -1.46 (1.26), residues: 12 loop : -0.21 (0.44), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 518 TYR 0.018 0.002 TYR A 50 PHE 0.010 0.001 PHE A 369 TRP 0.011 0.001 TRP A 473 HIS 0.010 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 5007) covalent geometry : angle 0.64183 ( 6803) SS BOND : bond 0.00226 ( 3) SS BOND : angle 0.79982 ( 6) hydrogen bonds : bond 0.03923 ( 225) hydrogen bonds : angle 4.74654 ( 645) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 HIS cc_start: 0.8606 (t-90) cc_final: 0.8281 (t-90) REVERT: A 82 MET cc_start: 0.7632 (tmm) cc_final: 0.6988 (tmm) REVERT: A 165 TRP cc_start: 0.3076 (t60) cc_final: 0.2195 (t60) REVERT: A 477 TRP cc_start: 0.7401 (OUTLIER) cc_final: 0.6154 (t-100) outliers start: 15 outliers final: 8 residues processed: 74 average time/residue: 0.0649 time to fit residues: 6.3087 Evaluate side-chains 66 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 545 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 53 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 17 optimal weight: 20.0000 chunk 30 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN A 340 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.105705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.089544 restraints weight = 18038.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.092324 restraints weight = 10437.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.094320 restraints weight = 7008.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.095544 restraints weight = 5177.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.096406 restraints weight = 4210.773| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 5010 Z= 0.209 Angle : 0.720 10.898 6809 Z= 0.362 Chirality : 0.045 0.144 710 Planarity : 0.005 0.043 881 Dihedral : 5.010 20.773 642 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.23 % Allowed : 23.34 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.35), residues: 595 helix: -0.29 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -0.48 (0.43), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 518 TYR 0.034 0.003 TYR A 237 PHE 0.012 0.002 PHE A 369 TRP 0.014 0.002 TRP A 473 HIS 0.012 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 5007) covalent geometry : angle 0.72000 ( 6803) SS BOND : bond 0.00429 ( 3) SS BOND : angle 1.08676 ( 6) hydrogen bonds : bond 0.04297 ( 225) hydrogen bonds : angle 4.86558 ( 645) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 HIS cc_start: 0.8812 (t-90) cc_final: 0.8556 (t-90) REVERT: A 82 MET cc_start: 0.7822 (tmm) cc_final: 0.7162 (tmm) REVERT: A 169 ARG cc_start: 0.7025 (mtt180) cc_final: 0.6654 (mtt180) REVERT: A 171 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7771 (pm20) REVERT: A 270 MET cc_start: 0.5220 (tpp) cc_final: 0.4798 (tpp) REVERT: A 477 TRP cc_start: 0.7633 (OUTLIER) cc_final: 0.6236 (t-100) REVERT: A 515 TYR cc_start: 0.8092 (m-10) cc_final: 0.7867 (m-10) outliers start: 17 outliers final: 10 residues processed: 77 average time/residue: 0.0695 time to fit residues: 6.9966 Evaluate side-chains 71 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 545 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 57 optimal weight: 5.9990 chunk 35 optimal weight: 20.0000 chunk 11 optimal weight: 0.2980 chunk 5 optimal weight: 7.9990 chunk 55 optimal weight: 0.0270 chunk 47 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 34 optimal weight: 40.0000 chunk 21 optimal weight: 6.9990 chunk 24 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 overall best weight: 3.2644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.107805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.091537 restraints weight = 18193.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.094374 restraints weight = 10613.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.096212 restraints weight = 7093.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.097456 restraints weight = 5341.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.098647 restraints weight = 4360.040| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 5010 Z= 0.158 Angle : 0.684 11.497 6809 Z= 0.340 Chirality : 0.043 0.165 710 Planarity : 0.004 0.041 881 Dihedral : 4.947 19.227 642 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.42 % Allowed : 24.48 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.36), residues: 595 helix: -0.22 (0.28), residues: 358 sheet: -1.05 (1.41), residues: 12 loop : -0.25 (0.46), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 393 TYR 0.021 0.002 TYR A 237 PHE 0.010 0.001 PHE A 452 TRP 0.012 0.002 TRP A 203 HIS 0.012 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 5007) covalent geometry : angle 0.68353 ( 6803) SS BOND : bond 0.00261 ( 3) SS BOND : angle 0.77437 ( 6) hydrogen bonds : bond 0.04017 ( 225) hydrogen bonds : angle 4.74985 ( 645) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 HIS cc_start: 0.8789 (t-90) cc_final: 0.8548 (t-90) REVERT: A 62 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.7123 (mtm) REVERT: A 82 MET cc_start: 0.7748 (tmm) cc_final: 0.7095 (tmm) REVERT: A 477 TRP cc_start: 0.7488 (OUTLIER) cc_final: 0.6145 (t-100) outliers start: 18 outliers final: 10 residues processed: 77 average time/residue: 0.0768 time to fit residues: 7.8110 Evaluate side-chains 69 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 545 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 1 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.107958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.091185 restraints weight = 18063.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.094199 restraints weight = 10603.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.096286 restraints weight = 7108.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.097050 restraints weight = 5283.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.098162 restraints weight = 4477.667| |-----------------------------------------------------------------------------| r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5010 Z= 0.147 Angle : 0.677 12.015 6809 Z= 0.332 Chirality : 0.043 0.156 710 Planarity : 0.004 0.039 881 Dihedral : 4.796 18.279 642 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.42 % Allowed : 24.10 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.36), residues: 595 helix: -0.12 (0.28), residues: 354 sheet: None (None), residues: 0 loop : -0.14 (0.44), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 518 TYR 0.026 0.002 TYR A 515 PHE 0.010 0.001 PHE A 504 TRP 0.012 0.001 TRP A 477 HIS 0.014 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 5007) covalent geometry : angle 0.67659 ( 6803) SS BOND : bond 0.00153 ( 3) SS BOND : angle 1.25324 ( 6) hydrogen bonds : bond 0.03851 ( 225) hydrogen bonds : angle 4.70110 ( 645) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 HIS cc_start: 0.8798 (t-90) cc_final: 0.8538 (t-90) REVERT: A 62 MET cc_start: 0.7346 (OUTLIER) cc_final: 0.6998 (mtm) REVERT: A 82 MET cc_start: 0.7844 (tmm) cc_final: 0.7136 (tmm) REVERT: A 297 MET cc_start: 0.7849 (mpp) cc_final: 0.7614 (mpp) REVERT: A 477 TRP cc_start: 0.7513 (OUTLIER) cc_final: 0.6319 (t-100) outliers start: 18 outliers final: 12 residues processed: 79 average time/residue: 0.0815 time to fit residues: 8.2890 Evaluate side-chains 73 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 545 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 20 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.108649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.091951 restraints weight = 18003.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.094880 restraints weight = 10565.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.097087 restraints weight = 7123.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.098290 restraints weight = 5261.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.099386 restraints weight = 4281.074| |-----------------------------------------------------------------------------| r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5010 Z= 0.140 Angle : 0.671 12.183 6809 Z= 0.329 Chirality : 0.042 0.159 710 Planarity : 0.004 0.039 881 Dihedral : 4.758 17.784 642 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.85 % Allowed : 26.19 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.36), residues: 595 helix: -0.06 (0.28), residues: 356 sheet: None (None), residues: 0 loop : -0.10 (0.45), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 518 TYR 0.036 0.002 TYR A 237 PHE 0.009 0.001 PHE A 504 TRP 0.010 0.001 TRP A 203 HIS 0.014 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 5007) covalent geometry : angle 0.67005 ( 6803) SS BOND : bond 0.00259 ( 3) SS BOND : angle 1.56967 ( 6) hydrogen bonds : bond 0.03846 ( 225) hydrogen bonds : angle 4.63585 ( 645) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 HIS cc_start: 0.8752 (t-90) cc_final: 0.8505 (t-90) REVERT: A 62 MET cc_start: 0.7342 (OUTLIER) cc_final: 0.6996 (mtm) REVERT: A 82 MET cc_start: 0.7843 (tmm) cc_final: 0.7165 (tmm) REVERT: A 171 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7439 (mp0) outliers start: 15 outliers final: 10 residues processed: 75 average time/residue: 0.0798 time to fit residues: 7.8446 Evaluate side-chains 71 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 545 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 58 optimal weight: 30.0000 chunk 21 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.106775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.090708 restraints weight = 17648.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.093601 restraints weight = 10239.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.095667 restraints weight = 6886.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.096806 restraints weight = 5086.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.097916 restraints weight = 4149.758| |-----------------------------------------------------------------------------| r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5010 Z= 0.184 Angle : 0.721 12.194 6809 Z= 0.357 Chirality : 0.045 0.179 710 Planarity : 0.004 0.039 881 Dihedral : 4.968 20.208 642 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.23 % Allowed : 26.76 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.35), residues: 595 helix: -0.18 (0.28), residues: 356 sheet: None (None), residues: 0 loop : -0.15 (0.44), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 518 TYR 0.032 0.002 TYR A 237 PHE 0.010 0.001 PHE A 308 TRP 0.016 0.002 TRP A 477 HIS 0.016 0.002 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 5007) covalent geometry : angle 0.72048 ( 6803) SS BOND : bond 0.00238 ( 3) SS BOND : angle 1.33818 ( 6) hydrogen bonds : bond 0.04129 ( 225) hydrogen bonds : angle 4.85061 ( 645) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 HIS cc_start: 0.8730 (t-90) cc_final: 0.8522 (t-90) REVERT: A 62 MET cc_start: 0.7448 (OUTLIER) cc_final: 0.7178 (mtm) REVERT: A 82 MET cc_start: 0.7828 (tmm) cc_final: 0.7205 (tmm) REVERT: A 165 TRP cc_start: 0.4310 (t60) cc_final: 0.4025 (t60) REVERT: A 171 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7529 (mp0) REVERT: A 360 MET cc_start: 0.6561 (mmm) cc_final: 0.6307 (mmm) REVERT: A 477 TRP cc_start: 0.7504 (OUTLIER) cc_final: 0.6081 (t-100) REVERT: A 481 LYS cc_start: 0.6923 (pttm) cc_final: 0.5718 (ttpt) outliers start: 17 outliers final: 10 residues processed: 75 average time/residue: 0.0752 time to fit residues: 7.4341 Evaluate side-chains 73 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 545 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.2487 > 50: distance: 20 - 72: 13.781 distance: 37 - 42: 26.201 distance: 42 - 43: 36.674 distance: 42 - 48: 39.629 distance: 43 - 44: 20.834 distance: 43 - 46: 34.466 distance: 44 - 45: 46.036 distance: 44 - 49: 11.093 distance: 46 - 47: 32.116 distance: 47 - 48: 9.880 distance: 49 - 50: 49.621 distance: 50 - 51: 21.006 distance: 50 - 53: 51.547 distance: 51 - 52: 34.050 distance: 51 - 58: 9.274 distance: 53 - 54: 37.516 distance: 54 - 55: 15.146 distance: 55 - 56: 28.851 distance: 55 - 57: 19.891 distance: 58 - 59: 15.511 distance: 59 - 60: 25.626 distance: 59 - 62: 11.004 distance: 60 - 61: 43.417 distance: 60 - 67: 18.061 distance: 62 - 63: 8.215 distance: 63 - 64: 9.890 distance: 64 - 65: 8.433 distance: 64 - 66: 10.391 distance: 67 - 68: 57.223 distance: 68 - 69: 39.733 distance: 68 - 71: 57.566 distance: 69 - 70: 7.307 distance: 69 - 73: 34.047 distance: 71 - 72: 25.689 distance: 73 - 74: 50.210 distance: 74 - 75: 17.807 distance: 74 - 77: 16.062 distance: 75 - 76: 18.474 distance: 75 - 81: 36.323 distance: 77 - 78: 40.450 distance: 78 - 79: 21.046 distance: 78 - 80: 31.091 distance: 81 - 82: 29.155 distance: 82 - 83: 37.805 distance: 82 - 85: 21.994 distance: 83 - 84: 37.249 distance: 83 - 89: 25.843 distance: 85 - 86: 16.899 distance: 86 - 88: 41.340 distance: 89 - 90: 37.940 distance: 90 - 91: 36.783 distance: 90 - 93: 35.580 distance: 91 - 92: 19.409 distance: 91 - 97: 32.194 distance: 93 - 94: 34.307 distance: 94 - 95: 56.028 distance: 94 - 96: 24.732 distance: 97 - 98: 35.279 distance: 98 - 99: 54.873 distance: 98 - 101: 52.039 distance: 99 - 100: 30.459 distance: 99 - 106: 35.109 distance: 101 - 102: 38.936 distance: 102 - 103: 22.274 distance: 103 - 104: 37.789 distance: 103 - 105: 37.196 distance: 106 - 107: 4.385 distance: 106 - 112: 8.009 distance: 107 - 108: 20.762 distance: 107 - 110: 33.719 distance: 108 - 109: 14.270 distance: 108 - 113: 22.099 distance: 110 - 111: 10.303 distance: 111 - 112: 24.205 distance: 113 - 114: 22.220 distance: 114 - 115: 37.059 distance: 115 - 116: 47.817 distance: 115 - 117: 18.873