Starting phenix.real_space_refine on Fri Aug 22 13:23:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tma_41382/08_2025/8tma_41382.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tma_41382/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8tma_41382/08_2025/8tma_41382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tma_41382/08_2025/8tma_41382.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tma_41382/08_2025/8tma_41382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tma_41382/08_2025/8tma_41382.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.009 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.07, per 1000 atoms: 0.33 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: 0.20 Conformation dependent library (CDL) restraints added in 171.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.10 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: 0.29 Time building geometry restraints manager: 0.29 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: 7.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.810 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.440 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (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 ARG 0.036 0.003 ARG A 408 TYR 0.020 0.003 TYR H 91 PHE 0.018 0.002 PHE H 29 TRP 0.014 0.002 TRP L 96 HIS 0.002 0.001 HIS H 40 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 3348) covalent geometry : angle 0.68163 ( 4557) SS BOND : bond 0.00818 ( 4) SS BOND : angle 1.34729 ( 8) hydrogen bonds : bond 0.27658 ( 100) hydrogen bonds : angle 9.40079 ( 252) *********************** 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 : 0.119 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: 0.0747 time to fit residues: 8.2355 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 : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.1980 chunk 37 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 L 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.135707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.113837 restraints weight = 5074.013| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.08 r_work: 0.3261 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3352 Z= 0.204 Angle : 0.686 6.027 4565 Z= 0.364 Chirality : 0.049 0.166 478 Planarity : 0.005 0.042 587 Dihedral : 5.046 44.429 456 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.98 % Allowed : 7.06 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.40), residues: 402 helix: -3.49 (0.59), residues: 31 sheet: 1.00 (0.50), residues: 121 loop : -1.25 (0.35), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 357 TYR 0.019 0.002 TYR H 91 PHE 0.017 0.002 PHE H 29 TRP 0.012 0.001 TRP L 96 HIS 0.003 0.001 HIS H 40 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 3348) covalent geometry : angle 0.68265 ( 4557) SS BOND : bond 0.00932 ( 4) SS BOND : angle 1.83209 ( 8) hydrogen bonds : bond 0.05046 ( 100) hydrogen bonds : angle 6.50003 ( 252) *********************** 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 64 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.072 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 60 average time/residue: 0.0587 time to fit residues: 4.1512 Evaluate side-chains 59 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.089 ------------------------------------------------------------------------------- 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 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 37 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN H 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.139934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.119327 restraints weight = 5189.571| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.06 r_work: 0.3367 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 3352 Z= 0.195 Angle : 0.655 5.568 4565 Z= 0.348 Chirality : 0.048 0.152 478 Planarity : 0.005 0.034 587 Dihedral : 5.347 55.597 456 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.39 % Allowed : 7.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.40), residues: 402 helix: -3.32 (0.66), residues: 31 sheet: 0.57 (0.45), residues: 144 loop : -1.27 (0.37), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 100E TYR 0.016 0.002 TYR H 91 PHE 0.016 0.002 PHE H 29 TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS H 101 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 3348) covalent geometry : angle 0.65096 ( 4557) SS BOND : bond 0.00920 ( 4) SS BOND : angle 1.90865 ( 8) hydrogen bonds : bond 0.04988 ( 100) hydrogen bonds : angle 6.19450 ( 252) *********************** 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 72 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.072 Fit side-chains revert: symmetry clash REVERT: L 107 LYS cc_start: 0.5752 (ttmt) cc_final: 0.5443 (tptp) outliers start: 12 outliers final: 10 residues processed: 66 average time/residue: 0.0553 time to fit residues: 4.3652 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 : 0.083 ------------------------------------------------------------------------------- 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 21 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 38 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.0970 chunk 16 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.133019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.111312 restraints weight = 5065.715| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.41 r_work: 0.3241 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3352 Z= 0.183 Angle : 0.627 5.328 4565 Z= 0.333 Chirality : 0.046 0.149 478 Planarity : 0.004 0.032 587 Dihedral : 5.130 46.406 456 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.24 % Allowed : 9.32 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.40), residues: 402 helix: -3.82 (0.68), residues: 25 sheet: 0.79 (0.44), residues: 145 loop : -1.17 (0.36), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 403 TYR 0.015 0.002 TYR H 91 PHE 0.014 0.002 PHE H 29 TRP 0.007 0.001 TRP A 436 HIS 0.004 0.002 HIS H 101 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 3348) covalent geometry : angle 0.62317 ( 4557) SS BOND : bond 0.00878 ( 4) SS BOND : angle 1.85803 ( 8) hydrogen bonds : bond 0.04718 ( 100) hydrogen bonds : angle 6.08964 ( 252) *********************** 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 71 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 107 LYS cc_start: 0.5716 (ttmt) cc_final: 0.5390 (tptp) outliers start: 15 outliers final: 12 residues processed: 65 average time/residue: 0.0470 time to fit residues: 3.7514 Evaluate side-chains 68 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.070 ------------------------------------------------------------------------------- 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 17 THR Chi-restraints excluded: chain H residue 21 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 31 optimal weight: 0.0870 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 3 optimal weight: 0.0980 chunk 23 optimal weight: 0.0000 chunk 24 optimal weight: 0.0980 chunk 16 optimal weight: 0.0270 chunk 22 optimal weight: 0.0980 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 overall best weight: 0.0620 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.139217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.117785 restraints weight = 5050.236| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.34 r_work: 0.3336 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3352 Z= 0.083 Angle : 0.479 5.423 4565 Z= 0.250 Chirality : 0.042 0.144 478 Planarity : 0.003 0.029 587 Dihedral : 4.183 36.400 456 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.54 % Allowed : 10.73 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.42), residues: 402 helix: -2.72 (0.92), residues: 25 sheet: 0.56 (0.43), residues: 166 loop : -0.39 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 403 TYR 0.009 0.001 TYR H 59 PHE 0.008 0.001 PHE A 377 TRP 0.010 0.001 TRP A 436 HIS 0.001 0.000 HIS H 77 Details of bonding type rmsd covalent geometry : bond 0.00176 ( 3348) covalent geometry : angle 0.47798 ( 4557) SS BOND : bond 0.00502 ( 4) SS BOND : angle 0.95461 ( 8) hydrogen bonds : bond 0.02770 ( 100) hydrogen bonds : angle 5.42584 ( 252) *********************** 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 71 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.120 Fit side-chains REVERT: A 511 VAL cc_start: 0.8940 (OUTLIER) cc_final: 0.8674 (t) REVERT: H 50 ASN cc_start: 0.9006 (m110) cc_final: 0.8771 (m110) REVERT: L 107 LYS cc_start: 0.5495 (ttmt) cc_final: 0.5099 (tptp) outliers start: 9 outliers final: 6 residues processed: 67 average time/residue: 0.0529 time to fit residues: 4.3105 Evaluate side-chains 60 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.137 ------------------------------------------------------------------------------- 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 511 VAL Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 78 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 5 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 0.0670 chunk 29 optimal weight: 0.5980 chunk 3 optimal weight: 0.3980 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.134632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.112676 restraints weight = 5068.104| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.46 r_work: 0.3260 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3352 Z= 0.140 Angle : 0.571 5.432 4565 Z= 0.297 Chirality : 0.044 0.145 478 Planarity : 0.004 0.029 587 Dihedral : 4.389 34.286 456 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.11 % Allowed : 12.71 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.41), residues: 402 helix: -3.60 (0.78), residues: 25 sheet: 0.69 (0.44), residues: 160 loop : -0.67 (0.38), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 403 TYR 0.013 0.001 TYR H 91 PHE 0.010 0.001 PHE H 53 TRP 0.006 0.001 TRP A 436 HIS 0.004 0.001 HIS H 101 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 3348) covalent geometry : angle 0.56764 ( 4557) SS BOND : bond 0.00710 ( 4) SS BOND : angle 1.52044 ( 8) hydrogen bonds : bond 0.04048 ( 100) hydrogen bonds : angle 5.69757 ( 252) *********************** 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 65 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: L 38 GLN cc_start: 0.9156 (OUTLIER) cc_final: 0.8019 (tt0) REVERT: L 107 LYS cc_start: 0.5585 (ttmt) cc_final: 0.5227 (tptp) outliers start: 11 outliers final: 8 residues processed: 60 average time/residue: 0.0599 time to fit residues: 4.3190 Evaluate side-chains 63 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 17 THR 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 38 GLN 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 15 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 0.3980 chunk 0 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 12 optimal weight: 0.4980 chunk 1 optimal weight: 0.3980 chunk 5 optimal weight: 0.2980 chunk 8 optimal weight: 0.3980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.134845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.112950 restraints weight = 5121.390| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.47 r_work: 0.3259 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3352 Z= 0.128 Angle : 0.552 5.360 4565 Z= 0.288 Chirality : 0.044 0.153 478 Planarity : 0.004 0.031 587 Dihedral : 4.355 32.973 456 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.39 % Allowed : 12.43 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.41), residues: 402 helix: -3.03 (0.75), residues: 31 sheet: 0.56 (0.43), residues: 163 loop : -0.62 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 403 TYR 0.013 0.001 TYR H 91 PHE 0.009 0.001 PHE H 53 TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS H 101 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 3348) covalent geometry : angle 0.54936 ( 4557) SS BOND : bond 0.00685 ( 4) SS BOND : angle 1.43258 ( 8) hydrogen bonds : bond 0.03804 ( 100) hydrogen bonds : angle 5.63298 ( 252) *********************** 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 67 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.075 Fit side-chains revert: symmetry clash REVERT: L 38 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.7861 (tt0) REVERT: L 107 LYS cc_start: 0.5407 (ttmt) cc_final: 0.5193 (tptp) outliers start: 12 outliers final: 9 residues processed: 61 average time/residue: 0.0523 time to fit residues: 3.8768 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 : 0.195 ------------------------------------------------------------------------------- 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 H residue 12 VAL Chi-restraints excluded: chain H residue 17 THR 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 38 GLN 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 19 optimal weight: 0.2980 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 0.0980 chunk 35 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 chunk 34 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 0.0670 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.134812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.113503 restraints weight = 5119.714| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.42 r_work: 0.3263 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3352 Z= 0.116 Angle : 0.533 5.466 4565 Z= 0.278 Chirality : 0.043 0.157 478 Planarity : 0.004 0.028 587 Dihedral : 4.268 31.692 456 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.54 % Allowed : 12.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.41), residues: 402 helix: -3.04 (0.75), residues: 31 sheet: 0.67 (0.44), residues: 158 loop : -0.62 (0.38), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 403 TYR 0.012 0.001 TYR H 91 PHE 0.008 0.001 PHE H 53 TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS H 101 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 3348) covalent geometry : angle 0.53029 ( 4557) SS BOND : bond 0.00633 ( 4) SS BOND : angle 1.36623 ( 8) hydrogen bonds : bond 0.03611 ( 100) hydrogen bonds : angle 5.57694 ( 252) *********************** 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 64 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.071 Fit side-chains revert: symmetry clash REVERT: L 100 GLN cc_start: 0.8529 (mp10) cc_final: 0.8317 (mp10) REVERT: L 107 LYS cc_start: 0.5447 (ttmt) cc_final: 0.5213 (tptp) outliers start: 9 outliers final: 8 residues processed: 59 average time/residue: 0.0512 time to fit residues: 3.6410 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 : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 17 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 30 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 27 optimal weight: 0.2980 chunk 0 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 13 optimal weight: 0.0000 overall best weight: 0.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.135094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.113324 restraints weight = 5124.152| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.34 r_work: 0.3262 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3996 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= 0.123 Angle : 0.564 8.730 4565 Z= 0.290 Chirality : 0.043 0.155 478 Planarity : 0.004 0.027 587 Dihedral : 4.223 30.749 456 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.11 % Allowed : 12.71 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.41), residues: 402 helix: -3.01 (0.76), residues: 31 sheet: 0.64 (0.44), residues: 163 loop : -0.67 (0.38), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 403 TYR 0.013 0.001 TYR H 91 PHE 0.009 0.001 PHE H 53 TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS H 101 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 3348) covalent geometry : angle 0.56115 ( 4557) SS BOND : bond 0.00640 ( 4) SS BOND : angle 1.39222 ( 8) hydrogen bonds : bond 0.03680 ( 100) hydrogen bonds : angle 5.60032 ( 252) *********************** 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: 11 poor density : 55 time to evaluate : 0.096 Fit side-chains revert: symmetry clash REVERT: L 107 LYS cc_start: 0.5483 (ttmt) cc_final: 0.5231 (tptp) outliers start: 11 outliers final: 10 residues processed: 60 average time/residue: 0.0793 time to fit residues: 5.6127 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 : 0.091 ------------------------------------------------------------------------------- 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 H residue 12 VAL Chi-restraints excluded: chain H residue 17 THR 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 19 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 chunk 6 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.132379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.110719 restraints weight = 5088.454| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.38 r_work: 0.3220 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3352 Z= 0.180 Angle : 0.617 6.203 4565 Z= 0.322 Chirality : 0.045 0.166 478 Planarity : 0.004 0.028 587 Dihedral : 4.710 36.233 456 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.11 % Allowed : 12.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.41), residues: 402 helix: -3.61 (0.78), residues: 25 sheet: 0.74 (0.44), residues: 155 loop : -0.81 (0.37), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 403 TYR 0.015 0.002 TYR H 91 PHE 0.012 0.001 PHE H 53 TRP 0.006 0.001 TRP A 353 HIS 0.006 0.002 HIS H 101 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 3348) covalent geometry : angle 0.61258 ( 4557) SS BOND : bond 0.00818 ( 4) SS BOND : angle 1.86496 ( 8) hydrogen bonds : bond 0.04573 ( 100) hydrogen bonds : angle 5.93193 ( 252) ********************** 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 66 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.072 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 10 residues processed: 60 average time/residue: 0.0646 time to fit residues: 4.6606 Evaluate side-chains 63 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.073 ------------------------------------------------------------------------------- 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 H residue 12 VAL Chi-restraints excluded: chain H residue 17 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 0.0070 chunk 26 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 0.0370 chunk 34 optimal weight: 2.9990 chunk 12 optimal weight: 0.0050 overall best weight: 0.2290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.135312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.114236 restraints weight = 5124.163| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.01 r_work: 0.3266 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4180 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= 0.106 Angle : 0.560 10.219 4565 Z= 0.287 Chirality : 0.043 0.158 478 Planarity : 0.003 0.028 587 Dihedral : 4.248 32.195 456 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.98 % Allowed : 13.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.41), residues: 402 helix: -2.93 (0.78), residues: 31 sheet: 0.78 (0.45), residues: 158 loop : -0.72 (0.37), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 403 TYR 0.010 0.001 TYR H 91 PHE 0.006 0.001 PHE H 53 TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS H 101 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 3348) covalent geometry : angle 0.55778 ( 4557) SS BOND : bond 0.00530 ( 4) SS BOND : angle 1.24124 ( 8) hydrogen bonds : bond 0.03305 ( 100) hydrogen bonds : angle 5.58101 ( 252) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1073.26 seconds wall clock time: 18 minutes 59.16 seconds (1139.16 seconds total)