Starting phenix.real_space_refine on Wed Jul 23 18:41:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r8k_19002/07_2025/8r8k_19002.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r8k_19002/07_2025/8r8k_19002.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r8k_19002/07_2025/8r8k_19002.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r8k_19002/07_2025/8r8k_19002.map" model { file = "/net/cci-nas-00/data/ceres_data/8r8k_19002/07_2025/8r8k_19002.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r8k_19002/07_2025/8r8k_19002.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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 17 5.16 5 C 2548 2.51 5 N 674 2.21 5 O 766 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 4005 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2222 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 17, 'TRANS': 262} Chain: "H" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 981 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "L" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 802 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Time building chain proxies: 4.57, per 1000 atoms: 1.14 Number of scatterers: 4005 At special positions: 0 Unit cell: (62.0755, 89.0966, 108.815, 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 17 16.00 O 766 8.00 N 674 7.00 C 2548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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: 0.98 Conformation dependent library (CDL) restraints added in 517.9 milliseconds 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 940 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 10 sheets defined 10.9% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 334 through 340 removed outlier: 3.531A pdb=" N VAL A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.520A pdb=" N TRP A 350 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 368 removed outlier: 3.771A pdb=" N VAL A 364 " --> pdb=" O ASP A 361 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N TYR A 366 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 387 removed outlier: 4.529A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU A 387 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 3.962A pdb=" N SER A 405 " --> pdb=" O ASN A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'H' and resid 53 through 57 Processing helix chain 'H' and resid 89 through 93 removed outlier: 4.188A pdb=" N THR H 93 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.125A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 314 through 316 Processing sheet with id=AA2, first strand: chain 'A' and resid 322 through 325 removed outlier: 5.740A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 572 " --> pdb=" O GLY A 563 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.508A pdb=" N TYR A 393 " --> pdb=" O SER A 511 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.848A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AA6, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.132A pdb=" N TRP H 33 " --> pdb=" O ASP H 101 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.460A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) 130 hydrogen bonds defined for protein. 300 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: 1.42 Time building geometry restraints manager: 1.19 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: 1287 1.34 - 1.46: 991 1.46 - 1.58: 1806 1.58 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 4104 Sorted by residual: bond pdb=" C GLN L 38 " pdb=" N LYS L 39 " ideal model delta sigma weight residual 1.331 1.310 0.021 2.83e-02 1.25e+03 5.55e-01 bond pdb=" CG PRO A 524 " pdb=" CD PRO A 524 " ideal model delta sigma weight residual 1.503 1.480 0.023 3.40e-02 8.65e+02 4.44e-01 bond pdb=" CA PHE H 105 " pdb=" C PHE H 105 " ideal model delta sigma weight residual 1.522 1.513 0.009 1.37e-02 5.33e+03 4.23e-01 bond pdb=" CA ILE A 431 " pdb=" CB ILE A 431 " ideal model delta sigma weight residual 1.540 1.532 0.008 1.23e-02 6.61e+03 4.11e-01 bond pdb=" N SER L 7 " pdb=" CA SER L 7 " ideal model delta sigma weight residual 1.457 1.448 0.009 1.41e-02 5.03e+03 4.01e-01 ... (remaining 4099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 5418 1.23 - 2.46: 111 2.46 - 3.69: 36 3.69 - 4.92: 3 4.92 - 6.15: 1 Bond angle restraints: 5569 Sorted by residual: angle pdb=" C HIS A 516 " pdb=" N ALA A 517 " pdb=" CA ALA A 517 " ideal model delta sigma weight residual 120.86 124.65 -3.79 1.60e+00 3.91e-01 5.60e+00 angle pdb=" N ASN A 484 " pdb=" CA ASN A 484 " pdb=" CB ASN A 484 " ideal model delta sigma weight residual 113.65 110.23 3.42 1.47e+00 4.63e-01 5.42e+00 angle pdb=" N ALA L 51 " pdb=" CA ALA L 51 " pdb=" CB ALA L 51 " ideal model delta sigma weight residual 113.65 110.43 3.22 1.47e+00 4.63e-01 4.80e+00 angle pdb=" C PRO A 370 " pdb=" N PHE A 371 " pdb=" CA PHE A 371 " ideal model delta sigma weight residual 121.97 125.24 -3.27 1.73e+00 3.34e-01 3.57e+00 angle pdb=" N PHE A 371 " pdb=" CA PHE A 371 " pdb=" C PHE A 371 " ideal model delta sigma weight residual 110.64 113.40 -2.76 1.48e+00 4.57e-01 3.48e+00 ... (remaining 5564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.55: 2087 14.55 - 29.10: 232 29.10 - 43.64: 68 43.64 - 58.19: 23 58.19 - 72.74: 15 Dihedral angle restraints: 2425 sinusoidal: 947 harmonic: 1478 Sorted by residual: dihedral pdb=" CB CYS A 388 " pdb=" SG CYS A 388 " pdb=" SG CYS A 522 " pdb=" CB CYS A 522 " ideal model delta sinusoidal sigma weight residual 93.00 124.82 -31.82 1 1.00e+01 1.00e-02 1.44e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 98 " pdb=" CB CYS H 98 " ideal model delta sinusoidal sigma weight residual 93.00 63.87 29.13 1 1.00e+01 1.00e-02 1.21e+01 dihedral pdb=" CA ASP L 70 " pdb=" CB ASP L 70 " pdb=" CG ASP L 70 " pdb=" OD1 ASP L 70 " ideal model delta sinusoidal sigma weight residual -30.00 -89.37 59.37 1 2.00e+01 2.50e-03 1.18e+01 ... (remaining 2422 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 367 0.031 - 0.062: 157 0.062 - 0.093: 44 0.093 - 0.124: 31 0.124 - 0.155: 3 Chirality restraints: 602 Sorted by residual: chirality pdb=" CB ILE A 431 " pdb=" CA ILE A 431 " pdb=" CG1 ILE A 431 " pdb=" CG2 ILE A 431 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.99e-01 chirality pdb=" CA ILE A 584 " pdb=" N ILE A 584 " pdb=" C ILE A 584 " pdb=" CB ILE A 584 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 chirality pdb=" CA ILE L 21 " pdb=" N ILE L 21 " pdb=" C ILE L 21 " pdb=" CB ILE L 21 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 ... (remaining 599 not shown) Planarity restraints: 724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 557 " -0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO A 558 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 558 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 558 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 369 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO A 370 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 370 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 370 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 371 " -0.008 2.00e-02 2.50e+03 8.43e-03 1.24e+00 pdb=" CG PHE A 371 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 PHE A 371 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 371 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 371 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 371 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 371 " 0.003 2.00e-02 2.50e+03 ... (remaining 721 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 89 2.70 - 3.25: 3703 3.25 - 3.80: 6041 3.80 - 4.35: 8203 4.35 - 4.90: 13968 Nonbonded interactions: 32004 Sorted by model distance: nonbonded pdb=" O THR A 390 " pdb=" OG1 THR A 520 " model vdw 2.145 3.040 nonbonded pdb=" O SER H 87 " pdb=" OG SER H 87 " model vdw 2.273 3.040 nonbonded pdb=" OD2 ASP A 395 " pdb=" OH TYR A 420 " model vdw 2.356 3.040 nonbonded pdb=" ND2 ASN A 402 " pdb=" O GLY A 501 " model vdw 2.364 3.120 nonbonded pdb=" OD1 ASP A 439 " pdb=" OH TYR L 31 " model vdw 2.384 3.040 ... (remaining 31999 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: 6.130 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.550 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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 : 0.003 0.023 4111 Z= 0.121 Angle : 0.493 6.145 5583 Z= 0.269 Chirality : 0.042 0.155 602 Planarity : 0.004 0.044 724 Dihedral : 15.085 72.737 1464 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.23 % Allowed : 17.73 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.18 (0.38), residues: 509 helix: -3.46 (0.70), residues: 29 sheet: 0.43 (0.42), residues: 173 loop : -0.01 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 433 HIS 0.000 0.000 HIS A 516 PHE 0.018 0.001 PHE A 371 TYR 0.008 0.001 TYR H 82 ARG 0.008 0.001 ARG A 564 Details of bonding type rmsd hydrogen bonds : bond 0.16382 ( 130) hydrogen bonds : angle 8.05532 ( 300) SS BOND : bond 0.00151 ( 7) SS BOND : angle 0.60075 ( 14) covalent geometry : bond 0.00261 ( 4104) covalent geometry : angle 0.49273 ( 5569) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.432 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 53 average time/residue: 0.1607 time to fit residues: 10.8738 Evaluate side-chains 48 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 0.0270 chunk 12 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 0.3980 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 45 optimal weight: 0.0970 overall best weight: 0.3836 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.143911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.121321 restraints weight = 5760.113| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.46 r_work: 0.3318 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4111 Z= 0.088 Angle : 0.450 5.046 5583 Z= 0.236 Chirality : 0.042 0.133 602 Planarity : 0.004 0.044 724 Dihedral : 3.548 13.836 562 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.50 % Allowed : 14.55 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.13 (0.38), residues: 509 helix: -3.83 (0.79), residues: 23 sheet: 0.46 (0.42), residues: 172 loop : -0.03 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 433 HIS 0.000 0.000 HIS A 516 PHE 0.006 0.001 PHE A 374 TYR 0.009 0.001 TYR H 82 ARG 0.006 0.000 ARG A 564 Details of bonding type rmsd hydrogen bonds : bond 0.02700 ( 130) hydrogen bonds : angle 5.99194 ( 300) SS BOND : bond 0.00135 ( 7) SS BOND : angle 0.53252 ( 14) covalent geometry : bond 0.00198 ( 4104) covalent geometry : angle 0.44935 ( 5569) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.465 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 54 average time/residue: 0.1798 time to fit residues: 12.2026 Evaluate side-chains 54 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 86 ASN Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 12 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3644 r_free = 0.3644 target = 0.136408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.114900 restraints weight = 5859.586| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.42 r_work: 0.3228 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4111 Z= 0.161 Angle : 0.483 4.806 5583 Z= 0.254 Chirality : 0.043 0.137 602 Planarity : 0.004 0.042 724 Dihedral : 3.791 14.929 560 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.18 % Allowed : 14.32 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.25 (0.38), residues: 509 helix: -3.92 (0.74), residues: 23 sheet: 0.31 (0.42), residues: 174 loop : -0.05 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 433 HIS 0.000 0.000 HIS A 516 PHE 0.018 0.001 PHE A 371 TYR 0.008 0.001 TYR A 450 ARG 0.005 0.000 ARG A 564 Details of bonding type rmsd hydrogen bonds : bond 0.02954 ( 130) hydrogen bonds : angle 5.86223 ( 300) SS BOND : bond 0.00199 ( 7) SS BOND : angle 0.60064 ( 14) covalent geometry : bond 0.00380 ( 4104) covalent geometry : angle 0.48302 ( 5569) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: H 78 LYS cc_start: 0.7670 (pttm) cc_final: 0.7318 (ptmm) outliers start: 14 outliers final: 9 residues processed: 59 average time/residue: 0.1670 time to fit residues: 12.3535 Evaluate side-chains 53 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 41 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.136488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.114404 restraints weight = 5879.422| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.51 r_work: 0.3223 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4111 Z= 0.129 Angle : 0.453 4.572 5583 Z= 0.239 Chirality : 0.043 0.141 602 Planarity : 0.004 0.039 724 Dihedral : 3.712 14.540 560 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.41 % Allowed : 15.23 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.27 (0.38), residues: 509 helix: -3.95 (0.72), residues: 23 sheet: 0.31 (0.42), residues: 173 loop : -0.08 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 433 HIS 0.000 0.000 HIS A 502 PHE 0.007 0.001 PHE A 512 TYR 0.007 0.001 TYR A 492 ARG 0.004 0.000 ARG A 564 Details of bonding type rmsd hydrogen bonds : bond 0.02654 ( 130) hydrogen bonds : angle 5.70083 ( 300) SS BOND : bond 0.00173 ( 7) SS BOND : angle 0.66282 ( 14) covalent geometry : bond 0.00304 ( 4104) covalent geometry : angle 0.45218 ( 5569) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: A 457 ASN cc_start: 0.8696 (m-40) cc_final: 0.8352 (m-40) REVERT: A 555 LYS cc_start: 0.5534 (pttm) cc_final: 0.3652 (tmtt) REVERT: H 78 LYS cc_start: 0.7609 (pttm) cc_final: 0.7282 (ptmm) outliers start: 15 outliers final: 11 residues processed: 59 average time/residue: 0.1894 time to fit residues: 13.9805 Evaluate side-chains 55 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 73 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 14 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3655 r_free = 0.3655 target = 0.137580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.115339 restraints weight = 5973.824| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.52 r_work: 0.3232 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4111 Z= 0.105 Angle : 0.434 4.510 5583 Z= 0.229 Chirality : 0.042 0.149 602 Planarity : 0.004 0.038 724 Dihedral : 3.564 14.073 560 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.86 % Allowed : 14.55 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.25 (0.38), residues: 509 helix: -3.95 (0.71), residues: 23 sheet: 0.31 (0.41), residues: 173 loop : -0.05 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 433 HIS 0.000 0.000 HIS A 516 PHE 0.020 0.001 PHE A 371 TYR 0.006 0.001 TYR A 492 ARG 0.003 0.000 ARG A 564 Details of bonding type rmsd hydrogen bonds : bond 0.02458 ( 130) hydrogen bonds : angle 5.53277 ( 300) SS BOND : bond 0.00125 ( 7) SS BOND : angle 0.55578 ( 14) covalent geometry : bond 0.00243 ( 4104) covalent geometry : angle 0.43357 ( 5569) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: A 457 ASN cc_start: 0.8695 (m-40) cc_final: 0.8345 (m-40) REVERT: A 526 LYS cc_start: 0.8443 (mmtt) cc_final: 0.8126 (ttpp) REVERT: A 555 LYS cc_start: 0.5466 (pttm) cc_final: 0.3621 (tmtt) REVERT: H 78 LYS cc_start: 0.7569 (pttm) cc_final: 0.7273 (ptmm) outliers start: 17 outliers final: 15 residues processed: 61 average time/residue: 0.1635 time to fit residues: 12.6498 Evaluate side-chains 59 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 77 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3656 r_free = 0.3656 target = 0.137871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.115463 restraints weight = 5862.557| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.52 r_work: 0.3235 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4111 Z= 0.115 Angle : 0.443 4.578 5583 Z= 0.232 Chirality : 0.043 0.189 602 Planarity : 0.004 0.039 724 Dihedral : 3.581 13.880 560 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.41 % Allowed : 15.45 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.22 (0.38), residues: 509 helix: -4.00 (0.69), residues: 23 sheet: 0.34 (0.41), residues: 172 loop : -0.03 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 433 HIS 0.000 0.000 HIS A 516 PHE 0.011 0.001 PHE A 371 TYR 0.007 0.001 TYR H 97 ARG 0.003 0.000 ARG A 564 Details of bonding type rmsd hydrogen bonds : bond 0.02489 ( 130) hydrogen bonds : angle 5.54021 ( 300) SS BOND : bond 0.00163 ( 7) SS BOND : angle 0.58705 ( 14) covalent geometry : bond 0.00271 ( 4104) covalent geometry : angle 0.44241 ( 5569) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 457 ASN cc_start: 0.8703 (m-40) cc_final: 0.8364 (m-40) REVERT: A 526 LYS cc_start: 0.8462 (mmtt) cc_final: 0.8151 (ttpp) REVERT: A 555 LYS cc_start: 0.5510 (pttm) cc_final: 0.3668 (tmtt) REVERT: H 78 LYS cc_start: 0.7570 (pttm) cc_final: 0.7283 (ptmm) outliers start: 15 outliers final: 14 residues processed: 60 average time/residue: 0.1639 time to fit residues: 12.5550 Evaluate side-chains 60 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 111 GLN ** 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 = 0.3651 r_free = 0.3651 target = 0.137452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.114966 restraints weight = 5927.730| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.53 r_work: 0.3233 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4111 Z= 0.121 Angle : 0.450 4.590 5583 Z= 0.236 Chirality : 0.042 0.147 602 Planarity : 0.003 0.036 724 Dihedral : 3.600 13.943 560 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.86 % Allowed : 15.23 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.27 (0.38), residues: 509 helix: -3.93 (0.74), residues: 23 sheet: 0.26 (0.41), residues: 173 loop : -0.04 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 433 HIS 0.000 0.000 HIS A 516 PHE 0.018 0.001 PHE A 371 TYR 0.007 0.001 TYR A 492 ARG 0.003 0.000 ARG A 564 Details of bonding type rmsd hydrogen bonds : bond 0.02545 ( 130) hydrogen bonds : angle 5.51158 ( 300) SS BOND : bond 0.00181 ( 7) SS BOND : angle 0.63212 ( 14) covalent geometry : bond 0.00285 ( 4104) covalent geometry : angle 0.44913 ( 5569) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 457 ASN cc_start: 0.8711 (m-40) cc_final: 0.8380 (m-40) REVERT: A 526 LYS cc_start: 0.8464 (mmtt) cc_final: 0.8162 (ttpp) REVERT: A 555 LYS cc_start: 0.5526 (pttm) cc_final: 0.3633 (tmtt) REVERT: H 78 LYS cc_start: 0.7584 (pttm) cc_final: 0.7316 (ptmm) outliers start: 17 outliers final: 15 residues processed: 63 average time/residue: 0.1902 time to fit residues: 14.7418 Evaluate side-chains 61 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 77 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 16 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 111 GLN ** 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 = 0.3644 r_free = 0.3644 target = 0.136637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.114800 restraints weight = 5815.970| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.45 r_work: 0.3231 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4111 Z= 0.133 Angle : 0.461 4.585 5583 Z= 0.241 Chirality : 0.043 0.163 602 Planarity : 0.003 0.035 724 Dihedral : 3.686 14.191 560 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.64 % Allowed : 15.00 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.31 (0.38), residues: 509 helix: -3.92 (0.75), residues: 23 sheet: 0.21 (0.41), residues: 173 loop : -0.06 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 433 HIS 0.000 0.000 HIS A 516 PHE 0.009 0.001 PHE A 371 TYR 0.007 0.001 TYR H 97 ARG 0.005 0.000 ARG A 564 Details of bonding type rmsd hydrogen bonds : bond 0.02572 ( 130) hydrogen bonds : angle 5.55603 ( 300) SS BOND : bond 0.00118 ( 7) SS BOND : angle 0.77701 ( 14) covalent geometry : bond 0.00315 ( 4104) covalent geometry : angle 0.46029 ( 5569) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: A 457 ASN cc_start: 0.8758 (m-40) cc_final: 0.8431 (m-40) REVERT: A 526 LYS cc_start: 0.8423 (mmtt) cc_final: 0.8139 (ttpp) REVERT: A 555 LYS cc_start: 0.5486 (pttm) cc_final: 0.3591 (tmtt) REVERT: H 78 LYS cc_start: 0.7599 (pttm) cc_final: 0.7331 (ptmm) outliers start: 16 outliers final: 16 residues processed: 63 average time/residue: 0.1570 time to fit residues: 12.6491 Evaluate side-chains 62 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 77 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 29 optimal weight: 0.0070 chunk 26 optimal weight: 0.0070 chunk 5 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 111 GLN ** 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 = 0.3656 r_free = 0.3656 target = 0.137779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.115543 restraints weight = 5959.084| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.51 r_work: 0.3233 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4111 Z= 0.121 Angle : 0.452 4.578 5583 Z= 0.237 Chirality : 0.042 0.152 602 Planarity : 0.004 0.036 724 Dihedral : 3.620 13.968 560 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.09 % Allowed : 14.77 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.29 (0.37), residues: 509 helix: -3.93 (0.74), residues: 23 sheet: 0.22 (0.41), residues: 173 loop : -0.05 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 433 HIS 0.000 0.000 HIS A 516 PHE 0.008 0.001 PHE A 371 TYR 0.007 0.001 TYR H 97 ARG 0.004 0.000 ARG A 564 Details of bonding type rmsd hydrogen bonds : bond 0.02556 ( 130) hydrogen bonds : angle 5.46896 ( 300) SS BOND : bond 0.00234 ( 7) SS BOND : angle 0.49986 ( 14) covalent geometry : bond 0.00286 ( 4104) covalent geometry : angle 0.45220 ( 5569) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 403 GLU cc_start: 0.8520 (tt0) cc_final: 0.8228 (tt0) REVERT: A 457 ASN cc_start: 0.8760 (m-40) cc_final: 0.8436 (m-40) REVERT: A 526 LYS cc_start: 0.8441 (mmtt) cc_final: 0.8156 (ttpp) REVERT: A 555 LYS cc_start: 0.5435 (pttm) cc_final: 0.3563 (tmtt) REVERT: H 78 LYS cc_start: 0.7585 (pttm) cc_final: 0.7317 (ptmm) outliers start: 18 outliers final: 16 residues processed: 63 average time/residue: 0.1846 time to fit residues: 14.5370 Evaluate side-chains 64 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 77 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 35 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 2 optimal weight: 0.0470 chunk 20 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 111 GLN ** 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 = 0.3654 r_free = 0.3654 target = 0.137560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.115876 restraints weight = 5817.245| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.45 r_work: 0.3245 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4111 Z= 0.106 Angle : 0.442 4.578 5583 Z= 0.232 Chirality : 0.042 0.136 602 Planarity : 0.003 0.035 724 Dihedral : 3.559 13.766 560 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.18 % Allowed : 16.36 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.28 (0.37), residues: 509 helix: -3.93 (0.74), residues: 23 sheet: 0.22 (0.41), residues: 172 loop : -0.03 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 433 HIS 0.000 0.000 HIS A 516 PHE 0.007 0.001 PHE A 374 TYR 0.007 0.001 TYR H 97 ARG 0.004 0.000 ARG A 564 Details of bonding type rmsd hydrogen bonds : bond 0.02478 ( 130) hydrogen bonds : angle 5.38999 ( 300) SS BOND : bond 0.00196 ( 7) SS BOND : angle 0.63796 ( 14) covalent geometry : bond 0.00249 ( 4104) covalent geometry : angle 0.44157 ( 5569) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 318 GLN cc_start: 0.8234 (mm110) cc_final: 0.7478 (mp10) REVERT: A 457 ASN cc_start: 0.8750 (m-40) cc_final: 0.8431 (m-40) REVERT: A 526 LYS cc_start: 0.8439 (mmtt) cc_final: 0.8162 (ttpp) REVERT: A 555 LYS cc_start: 0.5376 (pttm) cc_final: 0.3511 (tmtt) REVERT: H 78 LYS cc_start: 0.7581 (pttm) cc_final: 0.7305 (ptmm) outliers start: 14 outliers final: 14 residues processed: 58 average time/residue: 0.2373 time to fit residues: 17.0208 Evaluate side-chains 61 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 77 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 37 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 5 optimal weight: 0.0170 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 111 GLN ** 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 = 0.3655 r_free = 0.3655 target = 0.137482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.115865 restraints weight = 5822.289| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.42 r_work: 0.3243 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4111 Z= 0.118 Angle : 0.453 4.583 5583 Z= 0.237 Chirality : 0.042 0.138 602 Planarity : 0.003 0.036 724 Dihedral : 3.636 13.831 560 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.18 % Allowed : 16.82 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.28 (0.38), residues: 509 helix: -3.93 (0.74), residues: 23 sheet: 0.21 (0.41), residues: 173 loop : -0.02 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 433 HIS 0.000 0.000 HIS A 516 PHE 0.007 0.001 PHE A 540 TYR 0.007 0.001 TYR H 97 ARG 0.004 0.000 ARG A 564 Details of bonding type rmsd hydrogen bonds : bond 0.02523 ( 130) hydrogen bonds : angle 5.42939 ( 300) SS BOND : bond 0.00209 ( 7) SS BOND : angle 0.82624 ( 14) covalent geometry : bond 0.00281 ( 4104) covalent geometry : angle 0.45122 ( 5569) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2398.82 seconds wall clock time: 42 minutes 28.14 seconds (2548.14 seconds total)