Starting phenix.real_space_refine on Fri Jul 25 16:31:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k0k_22600/07_2025/7k0k_22600.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k0k_22600/07_2025/7k0k_22600.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k0k_22600/07_2025/7k0k_22600.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k0k_22600/07_2025/7k0k_22600.map" model { file = "/net/cci-nas-00/data/ceres_data/7k0k_22600/07_2025/7k0k_22600.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k0k_22600/07_2025/7k0k_22600.cif" } resolution = 2.6 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= 0.107 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 44 5.16 5 C 4875 2.51 5 N 1293 2.21 5 O 1402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 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: 7615 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3287 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 401} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3883 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 17, 'TRANS': 474} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 409 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 47} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'PLP': 1, 'VSD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 6.64, per 1000 atoms: 0.87 Number of scatterers: 7615 At special positions: 0 Unit cell: (90.1, 90.1, 114.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 1 15.00 O 1402 8.00 N 1293 7.00 C 4875 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 1.2 seconds 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1778 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 8 sheets defined 52.8% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 53 through 64 Processing helix chain 'A' and resid 77 through 81 Processing helix chain 'A' and resid 114 through 129 Processing helix chain 'A' and resid 142 through 156 Processing helix chain 'A' and resid 166 through 179 removed outlier: 4.466A pdb=" N ILE A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 192 through 202 Processing helix chain 'A' and resid 213 through 231 Processing helix chain 'A' and resid 231 through 238 removed outlier: 3.514A pdb=" N ALA A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 288 through 294 Processing helix chain 'A' and resid 296 through 300 Processing helix chain 'A' and resid 321 through 332 removed outlier: 4.729A pdb=" N HIS A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLN A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 342 through 359 Processing helix chain 'A' and resid 361 through 378 Processing helix chain 'A' and resid 404 through 421 Processing helix chain 'A' and resid 453 through 472 Processing helix chain 'B' and resid 67 through 94 removed outlier: 3.589A pdb=" N TRP B 94 " --> pdb=" O PHE B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 127 through 134 removed outlier: 3.510A pdb=" N ARG B 131 " --> pdb=" O MET B 128 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ASP B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 200 Processing helix chain 'B' and resid 213 through 228 Processing helix chain 'B' and resid 237 through 250 Proline residue: B 247 - end of helix Processing helix chain 'B' and resid 263 through 273 Processing helix chain 'B' and resid 284 through 299 Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 358 through 364 Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 391 through 402 Processing helix chain 'B' and resid 402 through 408 Processing helix chain 'B' and resid 412 through 427 Processing helix chain 'B' and resid 433 through 457 Processing helix chain 'B' and resid 475 through 489 removed outlier: 3.839A pdb=" N GLY B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 536 Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 25 through 29 Processing helix chain 'C' and resid 30 through 56 Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 95 removed outlier: 6.839A pdb=" N ALA A 425 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE A 101 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 164 removed outlier: 6.575A pdb=" N ILE A 271 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N SER A 304 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU A 273 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N ASN A 306 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N GLU A 245 " --> pdb=" O ASP A 188 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 383 through 386 removed outlier: 4.110A pdb=" N THR A 427 " --> pdb=" O ARG A 445 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 61 through 62 Processing sheet with id=AA5, first strand: chain 'B' and resid 145 through 152 removed outlier: 6.541A pdb=" N VAL B 146 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE B 167 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ILE B 148 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ASN B 165 " --> pdb=" O ILE B 148 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N GLU B 150 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N GLY B 492 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE B 171 " --> pdb=" O GLY B 492 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 231 through 235 removed outlier: 6.582A pdb=" N ILE B 310 " --> pdb=" O TYR B 340 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N TYR B 342 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE B 312 " --> pdb=" O TYR B 342 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ASP B 344 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL B 314 " --> pdb=" O ASP B 344 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N GLU B 315 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 317 through 318 Processing sheet with id=AA8, first strand: chain 'B' and resid 468 through 472 removed outlier: 3.755A pdb=" N VAL B 494 " --> pdb=" O ARG B 509 " (cutoff:3.500A) 413 hydrogen bonds defined for protein. 1161 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: 2.44 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1961 1.33 - 1.45: 1397 1.45 - 1.57: 4341 1.57 - 1.69: 1 1.69 - 1.81: 71 Bond restraints: 7771 Sorted by residual: bond pdb=" N ASN B 120 " pdb=" CA ASN B 120 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.26e-02 6.30e+03 6.95e+00 bond pdb=" N GLU B 119 " pdb=" CA GLU B 119 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.64e+00 bond pdb=" N PHE B 118 " pdb=" CA PHE B 118 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.27e-02 6.20e+03 5.54e+00 bond pdb=" N PHE B 121 " pdb=" CA PHE B 121 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.23e-02 6.61e+03 4.88e+00 bond pdb=" C09 VSD B 602 " pdb=" C10 VSD B 602 " ideal model delta sigma weight residual 1.525 1.569 -0.044 2.00e-02 2.50e+03 4.81e+00 ... (remaining 7766 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 10015 1.42 - 2.84: 392 2.84 - 4.25: 65 4.25 - 5.67: 17 5.67 - 7.09: 9 Bond angle restraints: 10498 Sorted by residual: angle pdb=" C LEU B 473 " pdb=" N TYR B 474 " pdb=" CA TYR B 474 " ideal model delta sigma weight residual 121.54 127.79 -6.25 1.91e+00 2.74e-01 1.07e+01 angle pdb=" N GLY A 315 " pdb=" CA GLY A 315 " pdb=" C GLY A 315 " ideal model delta sigma weight residual 111.85 115.12 -3.27 1.06e+00 8.90e-01 9.49e+00 angle pdb=" N GLU A 227 " pdb=" CA GLU A 227 " pdb=" CB GLU A 227 " ideal model delta sigma weight residual 110.28 114.72 -4.44 1.55e+00 4.16e-01 8.21e+00 angle pdb=" N GLY A 140 " pdb=" CA GLY A 140 " pdb=" C GLY A 140 " ideal model delta sigma weight residual 115.61 110.80 4.81 1.74e+00 3.30e-01 7.64e+00 angle pdb=" C PHE B 498 " pdb=" CA PHE B 498 " pdb=" CB PHE B 498 " ideal model delta sigma weight residual 112.76 107.79 4.97 1.86e+00 2.89e-01 7.13e+00 ... (remaining 10493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 4282 16.85 - 33.70: 318 33.70 - 50.55: 63 50.55 - 67.40: 12 67.40 - 84.24: 4 Dihedral angle restraints: 4679 sinusoidal: 1895 harmonic: 2784 Sorted by residual: dihedral pdb=" CA SER B 506 " pdb=" C SER B 506 " pdb=" N ARG B 507 " pdb=" CA ARG B 507 " ideal model delta harmonic sigma weight residual -180.00 -161.88 -18.12 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA THR B 400 " pdb=" C THR B 400 " pdb=" N HIS B 401 " pdb=" CA HIS B 401 " ideal model delta harmonic sigma weight residual -180.00 -161.92 -18.08 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA MET B 374 " pdb=" C MET B 374 " pdb=" N GLY B 375 " pdb=" CA GLY B 375 " ideal model delta harmonic sigma weight residual 180.00 162.19 17.81 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 4676 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 858 0.046 - 0.092: 227 0.092 - 0.138: 69 0.138 - 0.184: 2 0.184 - 0.230: 1 Chirality restraints: 1157 Sorted by residual: chirality pdb=" CB ILE B 503 " pdb=" CA ILE B 503 " pdb=" CG1 ILE B 503 " pdb=" CG2 ILE B 503 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB VAL B 416 " pdb=" CA VAL B 416 " pdb=" CG1 VAL B 416 " pdb=" CG2 VAL B 416 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.04e-01 chirality pdb=" CA PRO B 301 " pdb=" N PRO B 301 " pdb=" C PRO B 301 " pdb=" CB PRO B 301 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.93e-01 ... (remaining 1154 not shown) Planarity restraints: 1347 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 469 " -0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO B 470 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 470 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 470 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 412 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO B 413 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 413 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 413 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 111 " -0.011 2.00e-02 2.50e+03 1.43e-02 3.59e+00 pdb=" CG PHE B 111 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE B 111 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE B 111 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 111 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE B 111 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 111 " -0.002 2.00e-02 2.50e+03 ... (remaining 1344 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 31 2.51 - 3.11: 5623 3.11 - 3.71: 11876 3.71 - 4.30: 18250 4.30 - 4.90: 30102 Nonbonded interactions: 65882 Sorted by model distance: nonbonded pdb=" C4A PLP B 601 " pdb=" N21 VSD B 602 " model vdw 1.915 3.420 nonbonded pdb=" OE1 GLU A 275 " pdb=" OG SER A 278 " model vdw 2.190 3.040 nonbonded pdb=" C4 PLP B 601 " pdb=" N21 VSD B 602 " model vdw 2.261 3.340 nonbonded pdb=" OG1 THR B 355 " pdb=" OE2 GLU B 361 " model vdw 2.286 3.040 nonbonded pdb=" OH TYR B 448 " pdb=" OD1 ASP B 522 " model vdw 2.296 3.040 ... (remaining 65877 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 4.120 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.920 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 7772 Z= 0.261 Angle : 0.682 7.090 10498 Z= 0.393 Chirality : 0.045 0.230 1157 Planarity : 0.004 0.054 1347 Dihedral : 12.491 84.244 2901 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.26), residues: 958 helix: 1.08 (0.24), residues: 453 sheet: -0.02 (0.50), residues: 107 loop : -0.29 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 307 HIS 0.007 0.001 HIS B 403 PHE 0.031 0.002 PHE B 111 TYR 0.023 0.002 TYR A 166 ARG 0.009 0.001 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.15145 ( 413) hydrogen bonds : angle 6.12457 ( 1161) covalent geometry : bond 0.00583 ( 7771) covalent geometry : angle 0.68220 (10498) Misc. bond : bond 0.02750 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: A 225 GLU cc_start: 0.7286 (tt0) cc_final: 0.6895 (mt-10) REVERT: A 233 ARG cc_start: 0.6047 (mpp-170) cc_final: 0.5596 (ttm110) REVERT: B 464 GLU cc_start: 0.7386 (pt0) cc_final: 0.7176 (pt0) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 1.7402 time to fit residues: 180.1340 Evaluate side-chains 78 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 2.9990 chunk 72 optimal weight: 0.2980 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 55 optimal weight: 0.2980 chunk 86 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 HIS A 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.112576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.097787 restraints weight = 9531.701| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.68 r_work: 0.3160 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7772 Z= 0.161 Angle : 0.544 6.391 10498 Z= 0.291 Chirality : 0.044 0.165 1157 Planarity : 0.004 0.049 1347 Dihedral : 6.063 56.459 1083 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.24 % Allowed : 6.72 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.27), residues: 958 helix: 1.43 (0.24), residues: 462 sheet: 0.11 (0.53), residues: 93 loop : -0.09 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 134 HIS 0.008 0.001 HIS B 403 PHE 0.015 0.002 PHE B 280 TYR 0.018 0.001 TYR C 20 ARG 0.004 0.000 ARG B 151 Details of bonding type rmsd hydrogen bonds : bond 0.04768 ( 413) hydrogen bonds : angle 5.03158 ( 1161) covalent geometry : bond 0.00374 ( 7771) covalent geometry : angle 0.54428 (10498) Misc. bond : bond 0.00060 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 1.248 Fit side-chains REVERT: A 56 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7413 (mt-10) REVERT: A 150 ASP cc_start: 0.8292 (t70) cc_final: 0.8048 (t70) REVERT: A 225 GLU cc_start: 0.7813 (tt0) cc_final: 0.7099 (mt-10) REVERT: A 326 ASP cc_start: 0.8289 (m-30) cc_final: 0.7854 (m-30) REVERT: A 375 LYS cc_start: 0.8326 (tttm) cc_final: 0.8094 (tptp) REVERT: A 406 GLU cc_start: 0.7730 (pt0) cc_final: 0.7511 (tt0) REVERT: B 464 GLU cc_start: 0.7949 (pt0) cc_final: 0.7727 (pt0) REVERT: B 542 HIS cc_start: 0.7636 (m-70) cc_final: 0.7128 (m-70) outliers start: 10 outliers final: 3 residues processed: 94 average time/residue: 2.0704 time to fit residues: 204.6915 Evaluate side-chains 84 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 423 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 58 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3377 r_free = 0.3377 target = 0.112101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.097366 restraints weight = 9626.256| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.68 r_work: 0.3158 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7772 Z= 0.162 Angle : 0.524 6.360 10498 Z= 0.278 Chirality : 0.043 0.137 1157 Planarity : 0.004 0.048 1347 Dihedral : 5.867 60.201 1083 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.37 % Allowed : 8.71 % Favored : 89.93 % 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: 1.12 (0.27), residues: 958 helix: 1.65 (0.24), residues: 457 sheet: 0.09 (0.52), residues: 93 loop : -0.04 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 307 HIS 0.007 0.001 HIS B 403 PHE 0.015 0.002 PHE A 209 TYR 0.018 0.001 TYR C 20 ARG 0.004 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.04512 ( 413) hydrogen bonds : angle 4.81937 ( 1161) covalent geometry : bond 0.00385 ( 7771) covalent geometry : angle 0.52406 (10498) Misc. bond : bond 0.00081 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.865 Fit side-chains REVERT: A 150 ASP cc_start: 0.8255 (t70) cc_final: 0.8025 (t70) REVERT: A 225 GLU cc_start: 0.7841 (tt0) cc_final: 0.7126 (mt-10) REVERT: A 326 ASP cc_start: 0.8267 (m-30) cc_final: 0.7832 (m-30) REVERT: B 281 LYS cc_start: 0.8621 (mmtt) cc_final: 0.8182 (mtpt) REVERT: B 304 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7355 (mtm-85) REVERT: B 464 GLU cc_start: 0.7980 (pt0) cc_final: 0.7771 (pt0) REVERT: B 542 HIS cc_start: 0.7618 (m-70) cc_final: 0.7240 (m-70) outliers start: 11 outliers final: 6 residues processed: 91 average time/residue: 1.5014 time to fit residues: 143.5818 Evaluate side-chains 84 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain B residue 94 TRP Chi-restraints excluded: chain B residue 304 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 8 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 52 optimal weight: 0.0050 chunk 92 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- 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 = 0.3365 r_free = 0.3365 target = 0.111315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.096635 restraints weight = 9595.932| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.67 r_work: 0.3147 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7772 Z= 0.191 Angle : 0.540 6.357 10498 Z= 0.286 Chirality : 0.044 0.139 1157 Planarity : 0.004 0.049 1347 Dihedral : 5.767 61.010 1083 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.62 % Allowed : 9.83 % Favored : 88.56 % 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: 1.08 (0.27), residues: 958 helix: 1.63 (0.24), residues: 457 sheet: 0.06 (0.53), residues: 88 loop : -0.08 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 32 HIS 0.009 0.001 HIS B 403 PHE 0.016 0.002 PHE A 209 TYR 0.019 0.001 TYR C 20 ARG 0.006 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.04642 ( 413) hydrogen bonds : angle 4.77335 ( 1161) covalent geometry : bond 0.00458 ( 7771) covalent geometry : angle 0.54025 (10498) Misc. bond : bond 0.00094 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.895 Fit side-chains REVERT: A 150 ASP cc_start: 0.8247 (t70) cc_final: 0.8017 (t70) REVERT: A 225 GLU cc_start: 0.7857 (tt0) cc_final: 0.7139 (mt-10) REVERT: A 326 ASP cc_start: 0.8223 (m-30) cc_final: 0.7793 (m-30) REVERT: B 152 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8487 (pt0) REVERT: B 281 LYS cc_start: 0.8638 (mmtt) cc_final: 0.8186 (mtpt) REVERT: B 304 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7409 (mtm-85) REVERT: B 464 GLU cc_start: 0.8036 (pt0) cc_final: 0.7820 (pt0) outliers start: 13 outliers final: 7 residues processed: 88 average time/residue: 1.4035 time to fit residues: 130.2887 Evaluate side-chains 86 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain B residue 94 TRP Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 304 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 83 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 85 optimal weight: 0.0070 chunk 55 optimal weight: 0.0870 chunk 61 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 542 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.113043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.098358 restraints weight = 9490.371| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.68 r_work: 0.3170 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7772 Z= 0.126 Angle : 0.489 6.893 10498 Z= 0.260 Chirality : 0.042 0.137 1157 Planarity : 0.004 0.045 1347 Dihedral : 5.544 58.693 1083 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.62 % Allowed : 10.20 % Favored : 88.18 % 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: 1.26 (0.27), residues: 958 helix: 1.83 (0.24), residues: 457 sheet: 0.03 (0.53), residues: 88 loop : -0.04 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 32 HIS 0.005 0.001 HIS B 403 PHE 0.015 0.001 PHE A 209 TYR 0.019 0.001 TYR C 20 ARG 0.003 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.04008 ( 413) hydrogen bonds : angle 4.64932 ( 1161) covalent geometry : bond 0.00293 ( 7771) covalent geometry : angle 0.48916 (10498) Misc. bond : bond 0.00080 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: A 225 GLU cc_start: 0.7853 (tt0) cc_final: 0.7287 (mt-10) REVERT: A 326 ASP cc_start: 0.8182 (m-30) cc_final: 0.7744 (m-30) REVERT: B 206 THR cc_start: 0.8472 (OUTLIER) cc_final: 0.8208 (p) REVERT: B 281 LYS cc_start: 0.8620 (mmtt) cc_final: 0.8186 (mtpt) REVERT: B 304 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7327 (mtm-85) REVERT: B 464 GLU cc_start: 0.7997 (pt0) cc_final: 0.7782 (pt0) REVERT: B 530 GLU cc_start: 0.8146 (tt0) cc_final: 0.7937 (tt0) outliers start: 13 outliers final: 7 residues processed: 92 average time/residue: 1.3180 time to fit residues: 128.2316 Evaluate side-chains 89 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 94 TRP Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 496 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 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 469 GLN B 542 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.112220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.097549 restraints weight = 9562.036| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.67 r_work: 0.3160 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7772 Z= 0.157 Angle : 0.513 7.568 10498 Z= 0.270 Chirality : 0.043 0.138 1157 Planarity : 0.004 0.045 1347 Dihedral : 5.500 60.494 1083 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.74 % Allowed : 10.45 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.27), residues: 958 helix: 1.82 (0.24), residues: 457 sheet: 0.04 (0.53), residues: 88 loop : -0.07 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 32 HIS 0.007 0.001 HIS B 403 PHE 0.016 0.002 PHE A 209 TYR 0.019 0.001 TYR C 20 ARG 0.004 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.04242 ( 413) hydrogen bonds : angle 4.66007 ( 1161) covalent geometry : bond 0.00374 ( 7771) covalent geometry : angle 0.51286 (10498) Misc. bond : bond 0.00095 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.859 Fit side-chains revert: symmetry clash REVERT: A 181 ARG cc_start: 0.8576 (ttt180) cc_final: 0.8273 (ttm-80) REVERT: A 225 GLU cc_start: 0.7859 (tt0) cc_final: 0.7131 (mt-10) REVERT: A 326 ASP cc_start: 0.8182 (m-30) cc_final: 0.7746 (m-30) REVERT: B 206 THR cc_start: 0.8509 (OUTLIER) cc_final: 0.8241 (p) REVERT: B 281 LYS cc_start: 0.8618 (mmtt) cc_final: 0.8178 (mtpt) REVERT: B 304 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7359 (mtm-85) REVERT: B 464 GLU cc_start: 0.8015 (pt0) cc_final: 0.7799 (pt0) REVERT: B 530 GLU cc_start: 0.8129 (tt0) cc_final: 0.7922 (tt0) outliers start: 14 outliers final: 10 residues processed: 86 average time/residue: 1.3616 time to fit residues: 123.7264 Evaluate side-chains 92 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 94 TRP Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 496 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 28 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 542 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.114876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.100452 restraints weight = 9843.640| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.62 r_work: 0.3161 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7772 Z= 0.173 Angle : 0.526 9.178 10498 Z= 0.276 Chirality : 0.043 0.140 1157 Planarity : 0.004 0.046 1347 Dihedral : 5.501 61.482 1083 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.87 % Allowed : 10.95 % Favored : 87.19 % 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: 1.16 (0.27), residues: 958 helix: 1.77 (0.24), residues: 457 sheet: 0.03 (0.53), residues: 88 loop : -0.13 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 32 HIS 0.008 0.001 HIS B 403 PHE 0.016 0.002 PHE A 209 TYR 0.021 0.001 TYR C 20 ARG 0.004 0.000 ARG B 207 Details of bonding type rmsd hydrogen bonds : bond 0.04381 ( 413) hydrogen bonds : angle 4.67423 ( 1161) covalent geometry : bond 0.00413 ( 7771) covalent geometry : angle 0.52603 (10498) Misc. bond : bond 0.00091 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: A 181 ARG cc_start: 0.8598 (ttt180) cc_final: 0.8307 (ttm-80) REVERT: A 225 GLU cc_start: 0.7887 (tt0) cc_final: 0.7189 (mt-10) REVERT: A 326 ASP cc_start: 0.8192 (m-30) cc_final: 0.7757 (m-30) REVERT: B 206 THR cc_start: 0.8506 (OUTLIER) cc_final: 0.8263 (m) REVERT: B 281 LYS cc_start: 0.8632 (mmtt) cc_final: 0.8196 (mtpt) REVERT: B 304 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7386 (mtm-85) REVERT: B 464 GLU cc_start: 0.8026 (pt0) cc_final: 0.7814 (pt0) outliers start: 15 outliers final: 10 residues processed: 89 average time/residue: 1.3226 time to fit residues: 124.4357 Evaluate side-chains 91 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 94 TRP Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 496 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 28 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 63 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 542 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.115759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.101350 restraints weight = 9758.554| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.62 r_work: 0.3173 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7772 Z= 0.142 Angle : 0.508 10.094 10498 Z= 0.267 Chirality : 0.043 0.274 1157 Planarity : 0.004 0.048 1347 Dihedral : 5.409 60.520 1083 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.99 % Allowed : 10.82 % Favored : 87.19 % 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: 1.20 (0.27), residues: 958 helix: 1.82 (0.24), residues: 457 sheet: 0.01 (0.53), residues: 88 loop : -0.14 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 32 HIS 0.006 0.001 HIS B 403 PHE 0.015 0.001 PHE A 209 TYR 0.022 0.001 TYR C 20 ARG 0.003 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.04099 ( 413) hydrogen bonds : angle 4.63677 ( 1161) covalent geometry : bond 0.00335 ( 7771) covalent geometry : angle 0.50824 (10498) Misc. bond : bond 0.00088 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: A 181 ARG cc_start: 0.8598 (ttt180) cc_final: 0.8311 (ttm-80) REVERT: A 225 GLU cc_start: 0.7880 (tt0) cc_final: 0.7148 (mt-10) REVERT: A 233 ARG cc_start: 0.7019 (mtm110) cc_final: 0.6629 (pmm150) REVERT: A 326 ASP cc_start: 0.8191 (m-30) cc_final: 0.7761 (m-30) REVERT: B 206 THR cc_start: 0.8484 (OUTLIER) cc_final: 0.8226 (p) REVERT: B 281 LYS cc_start: 0.8632 (mmtt) cc_final: 0.8205 (mtpt) REVERT: B 304 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7419 (mtm-85) REVERT: B 464 GLU cc_start: 0.8013 (pt0) cc_final: 0.7801 (pt0) REVERT: B 530 GLU cc_start: 0.8194 (tt0) cc_final: 0.7962 (pt0) outliers start: 16 outliers final: 12 residues processed: 89 average time/residue: 1.3749 time to fit residues: 129.1639 Evaluate side-chains 94 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 94 TRP Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 496 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 58 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 52 optimal weight: 0.0470 chunk 71 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 542 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.116134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.101680 restraints weight = 9912.483| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.64 r_work: 0.3178 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7772 Z= 0.136 Angle : 0.504 10.681 10498 Z= 0.264 Chirality : 0.043 0.239 1157 Planarity : 0.004 0.050 1347 Dihedral : 5.334 61.425 1083 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.99 % Allowed : 10.95 % Favored : 87.06 % 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: 1.20 (0.27), residues: 958 helix: 1.81 (0.24), residues: 463 sheet: 0.01 (0.53), residues: 88 loop : -0.13 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 32 HIS 0.006 0.001 HIS B 403 PHE 0.015 0.001 PHE A 209 TYR 0.022 0.001 TYR C 20 ARG 0.004 0.000 ARG B 541 Details of bonding type rmsd hydrogen bonds : bond 0.04023 ( 413) hydrogen bonds : angle 4.59652 ( 1161) covalent geometry : bond 0.00319 ( 7771) covalent geometry : angle 0.50412 (10498) Misc. bond : bond 0.00089 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.882 Fit side-chains revert: symmetry clash REVERT: A 181 ARG cc_start: 0.8589 (ttt180) cc_final: 0.8305 (ttm-80) REVERT: A 225 GLU cc_start: 0.7874 (tt0) cc_final: 0.7208 (mt-10) REVERT: A 326 ASP cc_start: 0.8193 (m-30) cc_final: 0.7755 (m-30) REVERT: B 206 THR cc_start: 0.8482 (OUTLIER) cc_final: 0.8222 (p) REVERT: B 281 LYS cc_start: 0.8622 (mmtt) cc_final: 0.8195 (mtpt) REVERT: B 304 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7483 (mtm-85) REVERT: B 464 GLU cc_start: 0.8021 (pt0) cc_final: 0.7810 (pt0) REVERT: B 530 GLU cc_start: 0.8161 (tt0) cc_final: 0.7908 (pt0) outliers start: 16 outliers final: 11 residues processed: 93 average time/residue: 1.3335 time to fit residues: 131.0720 Evaluate side-chains 94 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 94 TRP Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 496 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 57 optimal weight: 0.2980 chunk 2 optimal weight: 0.0670 chunk 90 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 542 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.116690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.102166 restraints weight = 9901.159| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.65 r_work: 0.3187 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7772 Z= 0.122 Angle : 0.496 9.768 10498 Z= 0.259 Chirality : 0.042 0.240 1157 Planarity : 0.004 0.048 1347 Dihedral : 5.265 61.078 1083 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.74 % Allowed : 11.32 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.27), residues: 958 helix: 1.84 (0.24), residues: 463 sheet: -0.02 (0.52), residues: 88 loop : -0.13 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 134 HIS 0.005 0.001 HIS B 403 PHE 0.015 0.001 PHE A 209 TYR 0.023 0.001 TYR C 20 ARG 0.004 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.03875 ( 413) hydrogen bonds : angle 4.59979 ( 1161) covalent geometry : bond 0.00284 ( 7771) covalent geometry : angle 0.49602 (10498) Misc. bond : bond 0.00084 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: A 225 GLU cc_start: 0.7875 (tt0) cc_final: 0.7303 (mt-10) REVERT: A 233 ARG cc_start: 0.7016 (mtm110) cc_final: 0.6642 (pmm150) REVERT: A 326 ASP cc_start: 0.8207 (m-30) cc_final: 0.7783 (m-30) REVERT: B 206 THR cc_start: 0.8478 (OUTLIER) cc_final: 0.8217 (p) REVERT: B 281 LYS cc_start: 0.8617 (mmtt) cc_final: 0.8205 (mtpt) REVERT: B 304 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7466 (mtm-85) REVERT: B 464 GLU cc_start: 0.8017 (pt0) cc_final: 0.7806 (pt0) REVERT: B 472 MET cc_start: 0.9322 (mmm) cc_final: 0.9107 (mmp) REVERT: B 530 GLU cc_start: 0.8183 (tt0) cc_final: 0.7901 (pt0) outliers start: 14 outliers final: 10 residues processed: 89 average time/residue: 1.3432 time to fit residues: 126.4212 Evaluate side-chains 93 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 94 TRP Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 496 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 78 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 72 optimal weight: 0.0870 chunk 74 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 71 optimal weight: 0.3980 chunk 33 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 542 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.116838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.102362 restraints weight = 9821.040| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.65 r_work: 0.3191 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7772 Z= 0.119 Angle : 0.504 13.956 10498 Z= 0.259 Chirality : 0.042 0.227 1157 Planarity : 0.004 0.049 1347 Dihedral : 5.208 61.092 1083 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.74 % Allowed : 11.44 % Favored : 86.82 % 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: 1.25 (0.27), residues: 958 helix: 1.87 (0.24), residues: 463 sheet: -0.03 (0.52), residues: 88 loop : -0.12 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 134 HIS 0.005 0.001 HIS B 403 PHE 0.014 0.001 PHE A 209 TYR 0.022 0.001 TYR C 20 ARG 0.004 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 413) hydrogen bonds : angle 4.58601 ( 1161) covalent geometry : bond 0.00279 ( 7771) covalent geometry : angle 0.50448 (10498) Misc. bond : bond 0.00081 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5942.69 seconds wall clock time: 103 minutes 27.31 seconds (6207.31 seconds total)