Starting phenix.real_space_refine on Sat Apr 26 19:39:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tma_41382/04_2025/8tma_41382.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tma_41382/04_2025/8tma_41382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tma_41382/04_2025/8tma_41382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tma_41382/04_2025/8tma_41382.map" model { file = "/net/cci-nas-00/data/ceres_data/8tma_41382/04_2025/8tma_41382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tma_41382/04_2025/8tma_41382.cif" } resolution = 3.2 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= -0.009 sd= 0.098 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 11 5.16 5 C 2083 2.51 5 N 539 2.21 5 O 621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 3254 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1407 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1015 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 120} Chain: "L" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 832 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 4.40, per 1000 atoms: 1.35 Number of scatterers: 3254 At special positions: 0 Unit cell: (72.6, 86.9, 79.2, 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 11 16.00 O 621 8.00 N 539 7.00 C 2083 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 363.5 milliseconds 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 752 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 8 sheets defined 11.2% alpha, 38.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.570A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.490A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.415A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.754A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 357 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.606A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.614A pdb=" N VAL H 109 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.814A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASN H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.813A pdb=" N TRP H 35A" --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N TYR H 52 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N TYR H 34 " --> pdb=" O TYR H 52 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR H 35 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER H 35B" --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.628A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.185A pdb=" N GLN L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 10.044A pdb=" N SER L 67 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 12.317A pdb=" N ILE L 29 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 12.302A pdb=" N SER L 65 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.512A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.512A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 104 hydrogen bonds defined for protein. 252 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.85 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1026 1.34 - 1.46: 933 1.46 - 1.58: 1376 1.58 - 1.70: 0 1.70 - 1.82: 13 Bond restraints: 3348 Sorted by residual: bond pdb=" CG1 ILE A 434 " pdb=" CD1 ILE A 434 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.52e-01 bond pdb=" CB PRO A 337 " pdb=" CG PRO A 337 " ideal model delta sigma weight residual 1.492 1.535 -0.043 5.00e-02 4.00e+02 7.49e-01 bond pdb=" N ASN H 65 " pdb=" CA ASN H 65 " ideal model delta sigma weight residual 1.460 1.473 -0.013 1.54e-02 4.22e+03 7.00e-01 bond pdb=" CG LEU H 20 " pdb=" CD1 LEU H 20 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.93e-01 bond pdb=" SD MET L 4 " pdb=" CE MET L 4 " ideal model delta sigma weight residual 1.791 1.773 0.018 2.50e-02 1.60e+03 5.39e-01 ... (remaining 3343 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 4342 1.48 - 2.95: 186 2.95 - 4.43: 22 4.43 - 5.91: 6 5.91 - 7.39: 1 Bond angle restraints: 4557 Sorted by residual: angle pdb=" CB MET L 4 " pdb=" CG MET L 4 " pdb=" SD MET L 4 " ideal model delta sigma weight residual 112.70 105.31 7.39 3.00e+00 1.11e-01 6.06e+00 angle pdb=" C ASN H 64 " pdb=" N ASN H 65 " pdb=" CA ASN H 65 " ideal model delta sigma weight residual 122.46 125.80 -3.34 1.41e+00 5.03e-01 5.60e+00 angle pdb=" C ASP L 50 " pdb=" N ALA L 51 " pdb=" CA ALA L 51 " ideal model delta sigma weight residual 121.54 125.89 -4.35 1.91e+00 2.74e-01 5.19e+00 angle pdb=" CA CYS H 22 " pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " ideal model delta sigma weight residual 114.40 119.03 -4.63 2.30e+00 1.89e-01 4.06e+00 angle pdb=" CA CYS L 88 " pdb=" CB CYS L 88 " pdb=" SG CYS L 88 " ideal model delta sigma weight residual 114.40 118.60 -4.20 2.30e+00 1.89e-01 3.33e+00 ... (remaining 4552 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 1784 16.87 - 33.74: 135 33.74 - 50.61: 12 50.61 - 67.48: 5 67.48 - 84.35: 4 Dihedral angle restraints: 1940 sinusoidal: 752 harmonic: 1188 Sorted by residual: dihedral pdb=" CA GLN L 89 " pdb=" CB GLN L 89 " pdb=" CG GLN L 89 " pdb=" CD GLN L 89 " ideal model delta sinusoidal sigma weight residual -60.00 -114.44 54.44 3 1.50e+01 4.44e-03 9.28e+00 dihedral pdb=" CG ARG H 100A" pdb=" CD ARG H 100A" pdb=" NE ARG H 100A" pdb=" CZ ARG H 100A" ideal model delta sinusoidal sigma weight residual -90.00 -128.39 38.39 2 1.50e+01 4.44e-03 8.23e+00 dihedral pdb=" CA LEU L 33 " pdb=" CB LEU L 33 " pdb=" CG LEU L 33 " pdb=" CD1 LEU L 33 " ideal model delta sinusoidal sigma weight residual 180.00 135.68 44.32 3 1.50e+01 4.44e-03 7.97e+00 ... (remaining 1937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 250 0.032 - 0.063: 160 0.063 - 0.095: 34 0.095 - 0.127: 24 0.127 - 0.158: 10 Chirality restraints: 478 Sorted by residual: chirality pdb=" CA ILE A 434 " pdb=" N ILE A 434 " pdb=" C ILE A 434 " pdb=" CB ILE A 434 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.28e-01 chirality pdb=" CA ILE H 37 " pdb=" N ILE H 37 " pdb=" C ILE H 37 " pdb=" CB ILE H 37 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.50e-01 ... (remaining 475 not shown) Planarity restraints: 587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 408 " 0.320 9.50e-02 1.11e+02 1.45e-01 1.69e+01 pdb=" NE ARG A 408 " -0.031 2.00e-02 2.50e+03 pdb=" CZ ARG A 408 " 0.032 2.00e-02 2.50e+03 pdb=" NH1 ARG A 408 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG A 408 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 466 " 0.122 9.50e-02 1.11e+02 5.51e-02 2.31e+00 pdb=" NE ARG A 466 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 466 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 466 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 466 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 100A" 0.108 9.50e-02 1.11e+02 4.89e-02 1.95e+00 pdb=" NE ARG H 100A" -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG H 100A" 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG H 100A" -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG H 100A" -0.000 2.00e-02 2.50e+03 ... (remaining 584 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1109 2.84 - 3.35: 2644 3.35 - 3.87: 4739 3.87 - 4.38: 5348 4.38 - 4.90: 10154 Nonbonded interactions: 23994 Sorted by model distance: nonbonded pdb=" NH1 ARG A 457 " pdb=" O SER A 459 " model vdw 2.324 3.120 nonbonded pdb=" OE1 GLU A 406 " pdb=" NE2 GLN A 409 " model vdw 2.328 3.120 nonbonded pdb=" OG SER L 14 " pdb=" OD2 ASP L 17 " model vdw 2.345 3.040 nonbonded pdb=" OG SER A 349 " pdb=" O LEU A 452 " model vdw 2.380 3.040 nonbonded pdb=" NH2 ARG A 357 " pdb=" OD1 ASN A 394 " model vdw 2.394 3.120 ... (remaining 23989 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.700 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 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 0.043 3352 Z= 0.151 Angle : 0.683 7.387 4565 Z= 0.361 Chirality : 0.048 0.158 478 Planarity : 0.008 0.145 587 Dihedral : 12.057 84.349 1176 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.98 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.56 (0.39), residues: 402 helix: -4.09 (0.60), residues: 25 sheet: 0.34 (0.49), residues: 124 loop : -1.49 (0.33), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 96 HIS 0.002 0.001 HIS H 40 PHE 0.018 0.002 PHE H 29 TYR 0.020 0.003 TYR H 91 ARG 0.036 0.003 ARG A 408 Details of bonding type rmsd hydrogen bonds : bond 0.27658 ( 100) hydrogen bonds : angle 9.40079 ( 252) SS BOND : bond 0.00818 ( 4) SS BOND : angle 1.34729 ( 8) covalent geometry : bond 0.00366 ( 3348) covalent geometry : angle 0.68163 ( 4557) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: H 14 PRO cc_start: 0.6060 (Cg_endo) cc_final: 0.5845 (Cg_exo) REVERT: L 90 GLN cc_start: 0.8353 (pp30) cc_final: 0.7946 (pp30) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1777 time to fit residues: 19.6072 Evaluate side-chains 58 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 501 ASN H 6 GLN L 92 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.133520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.111887 restraints weight = 5073.108| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.39 r_work: 0.3244 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 3352 Z= 0.254 Angle : 0.752 6.423 4565 Z= 0.397 Chirality : 0.051 0.169 478 Planarity : 0.005 0.034 587 Dihedral : 5.600 53.015 456 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.98 % Allowed : 7.34 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.40), residues: 402 helix: -4.05 (0.57), residues: 25 sheet: 0.70 (0.47), residues: 134 loop : -1.46 (0.35), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 96 HIS 0.004 0.002 HIS H 101 PHE 0.022 0.003 PHE H 29 TYR 0.021 0.002 TYR H 91 ARG 0.003 0.001 ARG L 18 Details of bonding type rmsd hydrogen bonds : bond 0.05750 ( 100) hydrogen bonds : angle 6.56936 ( 252) SS BOND : bond 0.01066 ( 4) SS BOND : angle 2.02392 ( 8) covalent geometry : bond 0.00621 ( 3348) covalent geometry : angle 0.74751 ( 4557) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: H 14 PRO cc_start: 0.5826 (Cg_endo) cc_final: 0.5610 (Cg_exo) REVERT: L 107 LYS cc_start: 0.4942 (ttmt) cc_final: 0.4710 (tptp) outliers start: 7 outliers final: 7 residues processed: 63 average time/residue: 0.1736 time to fit residues: 13.1579 Evaluate side-chains 61 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.0980 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 21 optimal weight: 0.2980 chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 0.0060 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.136777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.114935 restraints weight = 5072.811| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.08 r_work: 0.3274 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3352 Z= 0.115 Angle : 0.566 5.599 4565 Z= 0.298 Chirality : 0.045 0.150 478 Planarity : 0.004 0.031 587 Dihedral : 4.923 49.649 456 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.26 % Allowed : 8.76 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.89 (0.41), residues: 402 helix: -3.13 (0.71), residues: 31 sheet: 0.62 (0.46), residues: 144 loop : -1.04 (0.38), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.001 0.001 HIS H 40 PHE 0.010 0.001 PHE A 377 TYR 0.011 0.001 TYR H 91 ARG 0.001 0.000 ARG A 408 Details of bonding type rmsd hydrogen bonds : bond 0.03821 ( 100) hydrogen bonds : angle 5.95410 ( 252) SS BOND : bond 0.00666 ( 4) SS BOND : angle 1.36563 ( 8) covalent geometry : bond 0.00259 ( 3348) covalent geometry : angle 0.56355 ( 4557) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: H 14 PRO cc_start: 0.5659 (Cg_endo) cc_final: 0.5431 (Cg_exo) REVERT: L 107 LYS cc_start: 0.5224 (ttmt) cc_final: 0.4848 (tptp) outliers start: 8 outliers final: 7 residues processed: 63 average time/residue: 0.1803 time to fit residues: 13.6704 Evaluate side-chains 63 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 16 optimal weight: 0.0270 chunk 6 optimal weight: 0.8980 chunk 37 optimal weight: 0.3980 chunk 36 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 overall best weight: 0.4638 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.134684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.113104 restraints weight = 5092.063| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.08 r_work: 0.3251 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3352 Z= 0.146 Angle : 0.579 5.179 4565 Z= 0.306 Chirality : 0.045 0.144 478 Planarity : 0.004 0.029 587 Dihedral : 4.819 45.186 456 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.82 % Allowed : 9.60 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.70 (0.41), residues: 402 helix: -3.62 (0.76), residues: 25 sheet: 0.84 (0.44), residues: 150 loop : -1.02 (0.37), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.002 0.001 HIS H 101 PHE 0.010 0.001 PHE H 29 TYR 0.014 0.002 TYR H 91 ARG 0.005 0.000 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.04166 ( 100) hydrogen bonds : angle 5.90705 ( 252) SS BOND : bond 0.00777 ( 4) SS BOND : angle 1.56652 ( 8) covalent geometry : bond 0.00346 ( 3348) covalent geometry : angle 0.57626 ( 4557) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 403 ARG cc_start: 0.8538 (ttp80) cc_final: 0.7986 (ttp80) REVERT: H 14 PRO cc_start: 0.5711 (Cg_endo) cc_final: 0.5496 (Cg_exo) REVERT: L 107 LYS cc_start: 0.5407 (ttmt) cc_final: 0.5041 (tptp) outliers start: 10 outliers final: 7 residues processed: 65 average time/residue: 0.1660 time to fit residues: 13.0818 Evaluate side-chains 63 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 0.0060 chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 7 optimal weight: 0.0970 overall best weight: 0.4394 ------------------------------------------------------------------------------- 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 = 0.3664 r_free = 0.3664 target = 0.134239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.112897 restraints weight = 5127.230| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.05 r_work: 0.3249 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3352 Z= 0.138 Angle : 0.567 5.262 4565 Z= 0.298 Chirality : 0.045 0.152 478 Planarity : 0.004 0.029 587 Dihedral : 4.598 37.427 456 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.82 % Allowed : 11.30 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.66 (0.41), residues: 402 helix: -3.57 (0.79), residues: 25 sheet: 0.58 (0.44), residues: 155 loop : -0.79 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS H 101 PHE 0.010 0.001 PHE A 377 TYR 0.014 0.001 TYR H 91 ARG 0.004 0.000 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.03983 ( 100) hydrogen bonds : angle 5.81033 ( 252) SS BOND : bond 0.00715 ( 4) SS BOND : angle 1.51683 ( 8) covalent geometry : bond 0.00325 ( 3348) covalent geometry : angle 0.56417 ( 4557) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.345 Fit side-chains REVERT: L 107 LYS cc_start: 0.5447 (ttmt) cc_final: 0.5221 (tptp) outliers start: 10 outliers final: 8 residues processed: 60 average time/residue: 0.1716 time to fit residues: 12.4970 Evaluate side-chains 63 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 21 optimal weight: 0.2980 chunk 22 optimal weight: 0.0020 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 0.0970 chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 overall best weight: 0.3186 ------------------------------------------------------------------------------- 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 = 0.3676 r_free = 0.3676 target = 0.135262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.113644 restraints weight = 5243.640| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.08 r_work: 0.3275 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3352 Z= 0.115 Angle : 0.530 5.459 4565 Z= 0.279 Chirality : 0.043 0.154 478 Planarity : 0.004 0.032 587 Dihedral : 4.325 34.259 456 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.11 % Allowed : 11.86 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.52 (0.41), residues: 402 helix: -3.53 (0.81), residues: 25 sheet: 0.68 (0.44), residues: 155 loop : -0.68 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.002 0.001 HIS H 101 PHE 0.008 0.001 PHE A 377 TYR 0.012 0.001 TYR H 91 ARG 0.006 0.000 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.03560 ( 100) hydrogen bonds : angle 5.64674 ( 252) SS BOND : bond 0.00641 ( 4) SS BOND : angle 1.30088 ( 8) covalent geometry : bond 0.00268 ( 3348) covalent geometry : angle 0.52723 ( 4557) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.407 Fit side-chains REVERT: A 403 ARG cc_start: 0.8462 (ttp80) cc_final: 0.7896 (ttp80) REVERT: A 511 VAL cc_start: 0.9047 (OUTLIER) cc_final: 0.8749 (t) REVERT: L 107 LYS cc_start: 0.5373 (ttmt) cc_final: 0.5154 (tptp) outliers start: 11 outliers final: 8 residues processed: 63 average time/residue: 0.1654 time to fit residues: 12.7998 Evaluate side-chains 64 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 38 optimal weight: 0.3980 chunk 4 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 18 optimal weight: 0.2980 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3650 r_free = 0.3650 target = 0.133447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.111976 restraints weight = 5091.659| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.04 r_work: 0.3249 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3352 Z= 0.143 Angle : 0.576 5.543 4565 Z= 0.301 Chirality : 0.044 0.151 478 Planarity : 0.004 0.028 587 Dihedral : 4.422 32.909 456 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.67 % Allowed : 11.86 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.52 (0.41), residues: 402 helix: -3.46 (0.85), residues: 25 sheet: 0.65 (0.45), residues: 155 loop : -0.66 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.004 0.001 HIS H 101 PHE 0.010 0.001 PHE H 53 TYR 0.014 0.001 TYR H 91 ARG 0.005 0.000 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.04040 ( 100) hydrogen bonds : angle 5.78401 ( 252) SS BOND : bond 0.00736 ( 4) SS BOND : angle 1.57258 ( 8) covalent geometry : bond 0.00341 ( 3348) covalent geometry : angle 0.57278 ( 4557) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 403 ARG cc_start: 0.8556 (ttp80) cc_final: 0.7937 (ttp80) REVERT: A 511 VAL cc_start: 0.8996 (OUTLIER) cc_final: 0.8696 (t) outliers start: 13 outliers final: 8 residues processed: 64 average time/residue: 0.1659 time to fit residues: 12.9626 Evaluate side-chains 64 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 15 optimal weight: 0.0570 chunk 23 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 = 0.3648 r_free = 0.3648 target = 0.132949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.111471 restraints weight = 5197.969| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.05 r_work: 0.3242 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3352 Z= 0.165 Angle : 0.597 5.294 4565 Z= 0.313 Chirality : 0.045 0.167 478 Planarity : 0.004 0.029 587 Dihedral : 4.663 35.445 456 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.39 % Allowed : 11.86 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.56 (0.41), residues: 402 helix: -3.49 (0.84), residues: 25 sheet: 0.62 (0.44), residues: 155 loop : -0.69 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.005 0.002 HIS H 101 PHE 0.011 0.001 PHE H 53 TYR 0.016 0.002 TYR H 91 ARG 0.005 0.001 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.04353 ( 100) hydrogen bonds : angle 5.91556 ( 252) SS BOND : bond 0.00787 ( 4) SS BOND : angle 1.75872 ( 8) covalent geometry : bond 0.00398 ( 3348) covalent geometry : angle 0.59310 ( 4557) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.382 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 64 average time/residue: 0.1771 time to fit residues: 13.7250 Evaluate side-chains 66 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 27 optimal weight: 0.7980 chunk 11 optimal weight: 0.1980 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 16 optimal weight: 0.3980 chunk 33 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 4 optimal weight: 0.0470 overall best weight: 0.4078 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.134418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.113070 restraints weight = 5185.456| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.04 r_work: 0.3261 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3352 Z= 0.134 Angle : 0.587 9.209 4565 Z= 0.304 Chirality : 0.044 0.158 478 Planarity : 0.004 0.032 587 Dihedral : 4.511 34.693 456 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.82 % Allowed : 12.43 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.50 (0.41), residues: 402 helix: -3.41 (0.86), residues: 25 sheet: 0.72 (0.45), residues: 155 loop : -0.71 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.004 0.001 HIS H 101 PHE 0.009 0.001 PHE H 53 TYR 0.014 0.001 TYR H 91 ARG 0.007 0.000 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.03843 ( 100) hydrogen bonds : angle 5.79979 ( 252) SS BOND : bond 0.00677 ( 4) SS BOND : angle 1.53456 ( 8) covalent geometry : bond 0.00322 ( 3348) covalent geometry : angle 0.58414 ( 4557) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.403 Fit side-chains REVERT: A 403 ARG cc_start: 0.8574 (ttp80) cc_final: 0.7860 (ttp80) outliers start: 10 outliers final: 10 residues processed: 62 average time/residue: 0.1799 time to fit residues: 13.4421 Evaluate side-chains 65 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 5 optimal weight: 0.0980 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 0.2980 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 0.1980 chunk 6 optimal weight: 0.6980 chunk 12 optimal weight: 0.0980 overall best weight: 0.2180 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.142191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.120577 restraints weight = 5176.650| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.15 r_work: 0.3381 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3352 Z= 0.100 Angle : 0.515 5.446 4565 Z= 0.269 Chirality : 0.042 0.151 478 Planarity : 0.004 0.029 587 Dihedral : 4.146 30.365 456 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.54 % Allowed : 12.15 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.43 (0.41), residues: 402 helix: -3.36 (0.87), residues: 25 sheet: 0.76 (0.45), residues: 155 loop : -0.65 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.002 0.001 HIS H 101 PHE 0.006 0.001 PHE H 53 TYR 0.010 0.001 TYR H 91 ARG 0.006 0.000 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.03231 ( 100) hydrogen bonds : angle 5.54110 ( 252) SS BOND : bond 0.00544 ( 4) SS BOND : angle 1.17949 ( 8) covalent geometry : bond 0.00229 ( 3348) covalent geometry : angle 0.51323 ( 4557) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.407 Fit side-chains REVERT: A 403 ARG cc_start: 0.8552 (ttp80) cc_final: 0.7882 (ttp80) REVERT: L 106 ILE cc_start: 0.7035 (OUTLIER) cc_final: 0.6745 (mt) outliers start: 9 outliers final: 8 residues processed: 60 average time/residue: 0.1702 time to fit residues: 12.4690 Evaluate side-chains 62 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 8 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 0.0970 chunk 23 optimal weight: 0.0980 chunk 28 optimal weight: 0.5980 chunk 22 optimal weight: 0.0980 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 overall best weight: 0.2978 ------------------------------------------------------------------------------- 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 = 0.3794 r_free = 0.3794 target = 0.141620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.119857 restraints weight = 5222.623| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.19 r_work: 0.3376 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3352 Z= 0.116 Angle : 0.568 10.656 4565 Z= 0.291 Chirality : 0.043 0.148 478 Planarity : 0.004 0.029 587 Dihedral : 4.137 29.461 456 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.54 % Allowed : 12.71 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.44 (0.41), residues: 402 helix: -3.35 (0.88), residues: 25 sheet: 0.79 (0.45), residues: 155 loop : -0.71 (0.37), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS H 101 PHE 0.008 0.001 PHE H 53 TYR 0.015 0.001 TYR H 34 ARG 0.006 0.000 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.03446 ( 100) hydrogen bonds : angle 5.57033 ( 252) SS BOND : bond 0.00610 ( 4) SS BOND : angle 1.31097 ( 8) covalent geometry : bond 0.00278 ( 3348) covalent geometry : angle 0.56543 ( 4557) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2558.32 seconds wall clock time: 44 minutes 23.92 seconds (2663.92 seconds total)