Starting phenix.real_space_refine on Sat May 10 00:45:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ynj_33963/05_2025/7ynj_33963.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ynj_33963/05_2025/7ynj_33963.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ynj_33963/05_2025/7ynj_33963.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ynj_33963/05_2025/7ynj_33963.map" model { file = "/net/cci-nas-00/data/ceres_data/7ynj_33963/05_2025/7ynj_33963.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ynj_33963/05_2025/7ynj_33963.cif" } resolution = 3.33 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= 0.003 sd= 0.075 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 33 5.16 5 C 2905 2.51 5 N 712 2.21 5 O 721 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 4371 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4145 Classifications: {'peptide': 564} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 26, 'TRANS': 537} Chain breaks: 3 Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 247 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 121 Chain: "B" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 26} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'GYP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.51, per 1000 atoms: 0.80 Number of scatterers: 4371 At special positions: 0 Unit cell: (74.711, 64.859, 88.668, 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 33 16.00 O 721 8.00 N 712 7.00 C 2905 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 255 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 345 " - pdb=" SG CYS A 351 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 517 " - pdb=" SG CYS A 522 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 574.1 milliseconds 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1078 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 0 sheets defined 81.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 26 through 46 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 77 through 91 Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 95 through 112 removed outlier: 4.023A pdb=" N GLU A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 103 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE A 104 " --> pdb=" O TRP A 100 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL A 105 " --> pdb=" O ASN A 101 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 120 removed outlier: 4.266A pdb=" N VAL A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 133 removed outlier: 3.723A pdb=" N TYR A 128 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 129 " --> pdb=" O MET A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 152 removed outlier: 4.314A pdb=" N ARG A 139 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 171 Processing helix chain 'A' and resid 173 through 192 Processing helix chain 'A' and resid 200 through 224 removed outlier: 3.630A pdb=" N HIS A 221 " --> pdb=" O GLY A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 231 Processing helix chain 'A' and resid 275 through 281 Processing helix chain 'A' and resid 281 through 291 removed outlier: 3.937A pdb=" N ILE A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 302 removed outlier: 3.590A pdb=" N VAL A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 323 removed outlier: 3.957A pdb=" N THR A 323 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 339 removed outlier: 4.309A pdb=" N MET A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) Proline residue: A 331 - end of helix Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 347 through 356 Processing helix chain 'A' and resid 364 through 373 Processing helix chain 'A' and resid 380 through 406 Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 418 through 446 Proline residue: A 442 - end of helix removed outlier: 4.149A pdb=" N ALA A 446 " --> pdb=" O PRO A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 450 Processing helix chain 'A' and resid 451 through 477 removed outlier: 3.514A pdb=" N TYR A 455 " --> pdb=" O GLN A 451 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR A 462 " --> pdb=" O ALA A 458 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) Proline residue: A 465 - end of helix Processing helix chain 'A' and resid 481 through 507 removed outlier: 3.686A pdb=" N GLY A 488 " --> pdb=" O GLY A 484 " (cutoff:3.500A) Proline residue: A 502 - end of helix Processing helix chain 'A' and resid 518 through 523 Processing helix chain 'A' and resid 525 through 547 Processing helix chain 'A' and resid 552 through 556 Processing helix chain 'A' and resid 560 through 564 removed outlier: 4.050A pdb=" N ARG A 564 " --> pdb=" O PHE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 671 Processing helix chain 'B' and resid 29 through 55 320 hydrogen bonds defined for protein. 948 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.21 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1318 1.34 - 1.46: 1174 1.46 - 1.58: 1950 1.58 - 1.70: 0 1.70 - 1.82: 49 Bond restraints: 4491 Sorted by residual: bond pdb=" C1 GYP A 701 " pdb=" O1 GYP A 701 " ideal model delta sigma weight residual 1.387 1.426 -0.039 2.00e-02 2.50e+03 3.90e+00 bond pdb=" C TYR A 366 " pdb=" N PRO A 367 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.30e-02 5.92e+03 3.48e+00 bond pdb=" C1 GYP A 701 " pdb=" O5 GYP A 701 " ideal model delta sigma weight residual 1.400 1.431 -0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" C2 GYP A 701 " pdb=" O2 GYP A 701 " ideal model delta sigma weight residual 1.402 1.430 -0.028 2.00e-02 2.50e+03 1.92e+00 bond pdb=" C6 GYP A 701 " pdb=" O6 GYP A 701 " ideal model delta sigma weight residual 1.407 1.432 -0.025 2.00e-02 2.50e+03 1.56e+00 ... (remaining 4486 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 6017 2.18 - 4.36: 115 4.36 - 6.55: 11 6.55 - 8.73: 3 8.73 - 10.91: 1 Bond angle restraints: 6147 Sorted by residual: angle pdb=" C LEU A 322 " pdb=" N THR A 323 " pdb=" CA THR A 323 " ideal model delta sigma weight residual 120.09 131.00 -10.91 1.25e+00 6.40e-01 7.62e+01 angle pdb=" N VAL A 346 " pdb=" CA VAL A 346 " pdb=" C VAL A 346 " ideal model delta sigma weight residual 113.71 109.69 4.02 9.50e-01 1.11e+00 1.79e+01 angle pdb=" N VAL A 248 " pdb=" CA VAL A 248 " pdb=" C VAL A 248 " ideal model delta sigma weight residual 113.53 109.83 3.70 9.80e-01 1.04e+00 1.43e+01 angle pdb=" N THR A 323 " pdb=" CA THR A 323 " pdb=" C THR A 323 " ideal model delta sigma weight residual 113.16 116.81 -3.65 1.42e+00 4.96e-01 6.62e+00 angle pdb=" C THR A 548 " pdb=" N ALA A 549 " pdb=" CA ALA A 549 " ideal model delta sigma weight residual 120.65 123.82 -3.17 1.36e+00 5.41e-01 5.44e+00 ... (remaining 6142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 2361 17.54 - 35.08: 163 35.08 - 52.62: 42 52.62 - 70.16: 3 70.16 - 87.70: 3 Dihedral angle restraints: 2572 sinusoidal: 884 harmonic: 1688 Sorted by residual: dihedral pdb=" CB CYS A 517 " pdb=" SG CYS A 517 " pdb=" SG CYS A 522 " pdb=" CB CYS A 522 " ideal model delta sinusoidal sigma weight residual -86.00 -154.35 68.35 1 1.00e+01 1.00e-02 6.06e+01 dihedral pdb=" CB CYS A 255 " pdb=" SG CYS A 255 " pdb=" SG CYS A 511 " pdb=" CB CYS A 511 " ideal model delta sinusoidal sigma weight residual 93.00 156.87 -63.87 1 1.00e+01 1.00e-02 5.37e+01 dihedral pdb=" CB CYS A 355 " pdb=" SG CYS A 355 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 145.25 -52.25 1 1.00e+01 1.00e-02 3.72e+01 ... (remaining 2569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 518 0.045 - 0.089: 183 0.089 - 0.134: 28 0.134 - 0.178: 3 0.178 - 0.223: 1 Chirality restraints: 733 Sorted by residual: chirality pdb=" CG LEU A 322 " pdb=" CB LEU A 322 " pdb=" CD1 LEU A 322 " pdb=" CD2 LEU A 322 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA PHE A 152 " pdb=" N PHE A 152 " pdb=" C PHE A 152 " pdb=" CB PHE A 152 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.68e-01 chirality pdb=" CA TRP A 65 " pdb=" N TRP A 65 " pdb=" C TRP A 65 " pdb=" CB TRP A 65 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.37e-01 ... (remaining 730 not shown) Planarity restraints: 748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 465 " -0.035 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO A 466 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 466 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 466 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 279 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.39e+00 pdb=" C LEU A 279 " 0.036 2.00e-02 2.50e+03 pdb=" O LEU A 279 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU A 280 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 501 " -0.033 5.00e-02 4.00e+02 5.03e-02 4.05e+00 pdb=" N PRO A 502 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 502 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 502 " -0.028 5.00e-02 4.00e+02 ... (remaining 745 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 975 2.78 - 3.31: 4495 3.31 - 3.84: 7593 3.84 - 4.37: 8107 4.37 - 4.90: 14496 Nonbonded interactions: 35666 Sorted by model distance: nonbonded pdb=" O ILE A 501 " pdb=" OG SER A 505 " model vdw 2.249 3.040 nonbonded pdb=" O PHE A 561 " pdb=" NH1 ARG A 564 " model vdw 2.267 3.120 nonbonded pdb=" OH TYR A 128 " pdb=" O LEU A 559 " model vdw 2.286 3.040 nonbonded pdb=" O PHE A 220 " pdb=" N GLY A 225 " model vdw 2.303 3.120 nonbonded pdb=" O GLY A 86 " pdb=" OG SER A 362 " model vdw 2.351 3.040 ... (remaining 35661 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: 1.290 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.370 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 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 : 0.004 0.046 4495 Z= 0.160 Angle : 0.680 10.909 6155 Z= 0.366 Chirality : 0.043 0.223 733 Planarity : 0.005 0.054 748 Dihedral : 12.776 87.697 1482 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.35), residues: 582 helix: 1.67 (0.26), residues: 417 sheet: None (None), residues: 0 loop : -0.94 (0.48), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 65 HIS 0.002 0.001 HIS A 555 PHE 0.012 0.001 PHE A 113 TYR 0.011 0.001 TYR A 128 ARG 0.007 0.001 ARG A 257 Details of bonding type rmsd hydrogen bonds : bond 0.13517 ( 320) hydrogen bonds : angle 6.39249 ( 948) SS BOND : bond 0.00044 ( 4) SS BOND : angle 1.18563 ( 8) covalent geometry : bond 0.00353 ( 4491) covalent geometry : angle 0.67896 ( 6147) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.460 Fit side-chains REVERT: A 325 MET cc_start: 0.6917 (tmm) cc_final: 0.5623 (tmm) REVERT: A 535 PHE cc_start: 0.6590 (m-80) cc_final: 0.6311 (m-10) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1318 time to fit residues: 15.3815 Evaluate side-chains 72 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.9980 chunk 43 optimal weight: 0.0970 chunk 24 optimal weight: 0.3980 chunk 15 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 52 optimal weight: 9.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.181226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.159404 restraints weight = 5260.005| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 2.34 r_work: 0.3822 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4495 Z= 0.143 Angle : 0.601 6.399 6155 Z= 0.307 Chirality : 0.043 0.158 733 Planarity : 0.005 0.048 748 Dihedral : 3.979 18.061 655 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.59 % Allowed : 8.02 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.36), residues: 582 helix: 1.61 (0.25), residues: 426 sheet: None (None), residues: 0 loop : -0.56 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 289 HIS 0.003 0.001 HIS A 80 PHE 0.026 0.002 PHE A 504 TYR 0.015 0.002 TYR A 339 ARG 0.005 0.001 ARG A 352 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 320) hydrogen bonds : angle 4.95184 ( 948) SS BOND : bond 0.00241 ( 4) SS BOND : angle 0.94065 ( 8) covalent geometry : bond 0.00341 ( 4491) covalent geometry : angle 0.59997 ( 6147) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 325 MET cc_start: 0.7251 (tmm) cc_final: 0.5919 (tmm) REVERT: A 535 PHE cc_start: 0.6669 (m-80) cc_final: 0.6433 (m-10) outliers start: 11 outliers final: 10 residues processed: 75 average time/residue: 0.1246 time to fit residues: 12.6899 Evaluate side-chains 78 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 655 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 10 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.172039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.150783 restraints weight = 5279.718| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.23 r_work: 0.3727 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 4495 Z= 0.200 Angle : 0.650 6.642 6155 Z= 0.337 Chirality : 0.045 0.158 733 Planarity : 0.005 0.048 748 Dihedral : 4.176 16.585 655 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.30 % Allowed : 14.86 % Favored : 81.84 % 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: 1.17 (0.35), residues: 582 helix: 1.29 (0.25), residues: 423 sheet: None (None), residues: 0 loop : -0.48 (0.55), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 289 HIS 0.003 0.001 HIS A 80 PHE 0.024 0.002 PHE A 504 TYR 0.016 0.002 TYR A 339 ARG 0.004 0.001 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.04113 ( 320) hydrogen bonds : angle 4.97726 ( 948) SS BOND : bond 0.00257 ( 4) SS BOND : angle 1.04890 ( 8) covalent geometry : bond 0.00492 ( 4491) covalent geometry : angle 0.64919 ( 6147) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 1.091 Fit side-chains REVERT: A 325 MET cc_start: 0.7529 (tmm) cc_final: 0.5974 (tmm) REVERT: A 328 MET cc_start: 0.6998 (mpp) cc_final: 0.6760 (mpp) outliers start: 14 outliers final: 11 residues processed: 80 average time/residue: 0.1254 time to fit residues: 13.6274 Evaluate side-chains 83 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 655 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 23 optimal weight: 0.0970 chunk 39 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.174468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.152851 restraints weight = 5355.626| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.26 r_work: 0.3756 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4495 Z= 0.148 Angle : 0.591 6.413 6155 Z= 0.304 Chirality : 0.042 0.143 733 Planarity : 0.005 0.047 748 Dihedral : 3.973 16.713 655 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.01 % Allowed : 16.51 % Favored : 79.48 % 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: 1.23 (0.35), residues: 582 helix: 1.33 (0.25), residues: 425 sheet: None (None), residues: 0 loop : -0.46 (0.55), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 289 HIS 0.003 0.001 HIS A 80 PHE 0.020 0.001 PHE A 504 TYR 0.013 0.002 TYR A 141 ARG 0.003 0.001 ARG A 564 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 320) hydrogen bonds : angle 4.79769 ( 948) SS BOND : bond 0.00242 ( 4) SS BOND : angle 0.95644 ( 8) covalent geometry : bond 0.00358 ( 4491) covalent geometry : angle 0.59010 ( 6147) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.484 Fit side-chains REVERT: A 448 GLN cc_start: 0.7528 (mm110) cc_final: 0.7293 (mm110) REVERT: A 655 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7146 (mm) outliers start: 17 outliers final: 13 residues processed: 85 average time/residue: 0.1398 time to fit residues: 15.7227 Evaluate side-chains 88 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 37 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 7 optimal weight: 0.0980 chunk 35 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4081 r_free = 0.4081 target = 0.175140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.153614 restraints weight = 5375.572| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.27 r_work: 0.3768 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4495 Z= 0.139 Angle : 0.600 8.220 6155 Z= 0.305 Chirality : 0.041 0.142 733 Planarity : 0.005 0.050 748 Dihedral : 3.898 17.246 655 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.72 % Allowed : 18.63 % Favored : 76.65 % 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: 1.28 (0.36), residues: 582 helix: 1.41 (0.25), residues: 423 sheet: None (None), residues: 0 loop : -0.57 (0.53), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 289 HIS 0.002 0.001 HIS A 80 PHE 0.019 0.002 PHE A 81 TYR 0.014 0.001 TYR A 671 ARG 0.006 0.001 ARG A 352 Details of bonding type rmsd hydrogen bonds : bond 0.03567 ( 320) hydrogen bonds : angle 4.71856 ( 948) SS BOND : bond 0.00221 ( 4) SS BOND : angle 0.88086 ( 8) covalent geometry : bond 0.00335 ( 4491) covalent geometry : angle 0.59917 ( 6147) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.446 Fit side-chains REVERT: A 448 GLN cc_start: 0.7543 (mm110) cc_final: 0.7301 (mm110) REVERT: A 655 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.7116 (mm) outliers start: 20 outliers final: 13 residues processed: 87 average time/residue: 0.1334 time to fit residues: 15.5617 Evaluate side-chains 86 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 37 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 7 optimal weight: 0.1980 chunk 32 optimal weight: 0.0770 chunk 18 optimal weight: 0.2980 chunk 38 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 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 = 0.4098 r_free = 0.4098 target = 0.177036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.155726 restraints weight = 5269.786| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.26 r_work: 0.3788 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4495 Z= 0.130 Angle : 0.575 8.958 6155 Z= 0.293 Chirality : 0.041 0.139 733 Planarity : 0.005 0.052 748 Dihedral : 3.806 16.109 655 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 5.19 % Allowed : 18.87 % Favored : 75.94 % 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: 1.42 (0.36), residues: 582 helix: 1.48 (0.25), residues: 426 sheet: None (None), residues: 0 loop : -0.44 (0.55), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 289 HIS 0.003 0.001 HIS A 80 PHE 0.026 0.001 PHE A 504 TYR 0.011 0.001 TYR A 141 ARG 0.004 0.001 ARG A 564 Details of bonding type rmsd hydrogen bonds : bond 0.03404 ( 320) hydrogen bonds : angle 4.63764 ( 948) SS BOND : bond 0.00217 ( 4) SS BOND : angle 0.84112 ( 8) covalent geometry : bond 0.00308 ( 4491) covalent geometry : angle 0.57505 ( 6147) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.445 Fit side-chains REVERT: A 64 TRP cc_start: 0.8280 (p-90) cc_final: 0.7979 (p-90) REVERT: A 448 GLN cc_start: 0.7559 (mm110) cc_final: 0.7321 (mm110) REVERT: A 655 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7159 (mm) outliers start: 22 outliers final: 14 residues processed: 87 average time/residue: 0.1267 time to fit residues: 14.7294 Evaluate side-chains 91 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 37 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 0.2980 chunk 40 optimal weight: 0.0670 chunk 48 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 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 = 0.4095 r_free = 0.4095 target = 0.176730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.155023 restraints weight = 5310.549| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 2.33 r_work: 0.3780 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4495 Z= 0.131 Angle : 0.574 6.214 6155 Z= 0.292 Chirality : 0.041 0.141 733 Planarity : 0.005 0.052 748 Dihedral : 3.801 15.457 655 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.25 % Allowed : 20.75 % Favored : 75.00 % 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: 1.48 (0.36), residues: 582 helix: 1.53 (0.25), residues: 425 sheet: None (None), residues: 0 loop : -0.45 (0.55), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 289 HIS 0.003 0.001 HIS A 80 PHE 0.024 0.001 PHE A 504 TYR 0.012 0.001 TYR A 141 ARG 0.004 0.001 ARG A 352 Details of bonding type rmsd hydrogen bonds : bond 0.03381 ( 320) hydrogen bonds : angle 4.59621 ( 948) SS BOND : bond 0.00206 ( 4) SS BOND : angle 0.77852 ( 8) covalent geometry : bond 0.00312 ( 4491) covalent geometry : angle 0.57356 ( 6147) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.480 Fit side-chains REVERT: A 64 TRP cc_start: 0.8281 (p-90) cc_final: 0.8010 (p-90) REVERT: A 151 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7694 (mp) REVERT: A 448 GLN cc_start: 0.7587 (mm110) cc_final: 0.7326 (mm110) REVERT: A 655 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7163 (mm) outliers start: 18 outliers final: 15 residues processed: 86 average time/residue: 0.1521 time to fit residues: 17.2732 Evaluate side-chains 88 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 37 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 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 = 0.4051 r_free = 0.4051 target = 0.172520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.150780 restraints weight = 5341.211| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.31 r_work: 0.3720 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4495 Z= 0.164 Angle : 0.624 8.320 6155 Z= 0.318 Chirality : 0.043 0.149 733 Planarity : 0.005 0.051 748 Dihedral : 3.971 15.882 655 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.48 % Allowed : 22.17 % Favored : 73.35 % 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: 1.27 (0.36), residues: 582 helix: 1.35 (0.25), residues: 425 sheet: None (None), residues: 0 loop : -0.43 (0.55), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 289 HIS 0.002 0.001 HIS A 80 PHE 0.024 0.002 PHE A 504 TYR 0.016 0.002 TYR A 671 ARG 0.007 0.001 ARG A 257 Details of bonding type rmsd hydrogen bonds : bond 0.03760 ( 320) hydrogen bonds : angle 4.71329 ( 948) SS BOND : bond 0.00234 ( 4) SS BOND : angle 0.90293 ( 8) covalent geometry : bond 0.00401 ( 4491) covalent geometry : angle 0.62361 ( 6147) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.508 Fit side-chains REVERT: A 64 TRP cc_start: 0.8336 (p-90) cc_final: 0.7977 (p-90) REVERT: A 151 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7712 (mp) REVERT: A 448 GLN cc_start: 0.7568 (mm110) cc_final: 0.7291 (mm110) REVERT: A 655 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.7115 (mm) outliers start: 19 outliers final: 15 residues processed: 85 average time/residue: 0.1209 time to fit residues: 14.1729 Evaluate side-chains 90 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 37 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 0.6980 chunk 21 optimal weight: 0.2980 chunk 8 optimal weight: 0.0270 chunk 54 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 2 optimal weight: 0.4980 chunk 49 optimal weight: 0.5980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 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 = 0.4096 r_free = 0.4096 target = 0.177013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.155431 restraints weight = 5347.685| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.29 r_work: 0.3774 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4495 Z= 0.130 Angle : 0.594 8.230 6155 Z= 0.299 Chirality : 0.042 0.136 733 Planarity : 0.005 0.051 748 Dihedral : 3.838 16.108 655 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.48 % Allowed : 22.17 % Favored : 73.35 % 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: 1.48 (0.36), residues: 582 helix: 1.54 (0.25), residues: 425 sheet: None (None), residues: 0 loop : -0.46 (0.55), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 289 HIS 0.002 0.001 HIS A 80 PHE 0.023 0.001 PHE A 504 TYR 0.011 0.001 TYR A 141 ARG 0.006 0.001 ARG A 257 Details of bonding type rmsd hydrogen bonds : bond 0.03397 ( 320) hydrogen bonds : angle 4.56013 ( 948) SS BOND : bond 0.00203 ( 4) SS BOND : angle 0.80758 ( 8) covalent geometry : bond 0.00306 ( 4491) covalent geometry : angle 0.59349 ( 6147) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.466 Fit side-chains REVERT: A 64 TRP cc_start: 0.8267 (p-90) cc_final: 0.7968 (p-90) REVERT: A 151 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.7657 (mp) REVERT: A 448 GLN cc_start: 0.7590 (mm110) cc_final: 0.7320 (mm110) REVERT: A 655 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.7146 (mm) outliers start: 19 outliers final: 16 residues processed: 88 average time/residue: 0.1455 time to fit residues: 16.7555 Evaluate side-chains 90 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 37 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 35 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 2 optimal weight: 0.0980 chunk 55 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 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 = 0.4073 r_free = 0.4073 target = 0.174925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.153546 restraints weight = 5241.962| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.24 r_work: 0.3764 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4495 Z= 0.147 Angle : 0.615 8.431 6155 Z= 0.310 Chirality : 0.042 0.143 733 Planarity : 0.005 0.050 748 Dihedral : 3.923 16.064 655 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.25 % Allowed : 22.41 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.36), residues: 582 helix: 1.59 (0.25), residues: 419 sheet: None (None), residues: 0 loop : -0.50 (0.54), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 289 HIS 0.002 0.001 HIS A 80 PHE 0.022 0.001 PHE A 504 TYR 0.012 0.001 TYR A 141 ARG 0.008 0.001 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.03528 ( 320) hydrogen bonds : angle 4.60383 ( 948) SS BOND : bond 0.00201 ( 4) SS BOND : angle 0.75582 ( 8) covalent geometry : bond 0.00355 ( 4491) covalent geometry : angle 0.61493 ( 6147) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.450 Fit side-chains REVERT: A 64 TRP cc_start: 0.8275 (p-90) cc_final: 0.7981 (p-90) REVERT: A 151 ILE cc_start: 0.7926 (OUTLIER) cc_final: 0.7715 (mp) REVERT: A 328 MET cc_start: 0.6585 (mpp) cc_final: 0.6087 (mtt) REVERT: A 448 GLN cc_start: 0.7541 (mm110) cc_final: 0.7269 (mm110) REVERT: A 655 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.7109 (mm) outliers start: 18 outliers final: 16 residues processed: 85 average time/residue: 0.1162 time to fit residues: 13.6483 Evaluate side-chains 91 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 37 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 21 optimal weight: 0.1980 chunk 57 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 44 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 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 = 0.4093 r_free = 0.4093 target = 0.176795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.154928 restraints weight = 5324.522| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.34 r_work: 0.3774 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4495 Z= 0.135 Angle : 0.604 8.421 6155 Z= 0.304 Chirality : 0.041 0.139 733 Planarity : 0.005 0.051 748 Dihedral : 3.881 16.323 655 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.48 % Allowed : 22.17 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.36), residues: 582 helix: 1.68 (0.25), residues: 419 sheet: None (None), residues: 0 loop : -0.55 (0.54), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 289 HIS 0.001 0.001 HIS A 80 PHE 0.022 0.001 PHE A 504 TYR 0.012 0.001 TYR A 141 ARG 0.009 0.001 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.03383 ( 320) hydrogen bonds : angle 4.53627 ( 948) SS BOND : bond 0.00189 ( 4) SS BOND : angle 0.71746 ( 8) covalent geometry : bond 0.00321 ( 4491) covalent geometry : angle 0.60393 ( 6147) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2247.29 seconds wall clock time: 39 minutes 44.07 seconds (2384.07 seconds total)