Starting phenix.real_space_refine on Tue Feb 3 13:14:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xqb_67107/02_2026/9xqb_67107.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xqb_67107/02_2026/9xqb_67107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xqb_67107/02_2026/9xqb_67107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xqb_67107/02_2026/9xqb_67107.map" model { file = "/net/cci-nas-00/data/ceres_data/9xqb_67107/02_2026/9xqb_67107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xqb_67107/02_2026/9xqb_67107.cif" } resolution = 3.45 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= 0.000 sd= 0.008 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 3 5.16 5 C 1839 2.51 5 N 521 2.21 5 O 569 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2932 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 786 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 1237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1237 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 140} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain breaks: 3 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 498 Unresolved non-hydrogen angles: 659 Unresolved non-hydrogen dihedrals: 424 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'TYR:plan': 5, 'GLU:plan': 4, 'ASN:plan1': 11, 'TRP:plan': 5, 'GLN:plan1': 5, 'ASP:plan': 2, 'PHE:plan': 12, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 242 Chain: "A" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 909 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain breaks: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 56 Time building chain proxies: 0.85, per 1000 atoms: 0.29 Number of scatterers: 2932 At special positions: 0 Unit cell: (57, 66, 114.75, 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 3 16.00 O 569 8.00 N 521 7.00 C 1839 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.23 Conformation dependent library (CDL) restraints added in 132.0 milliseconds 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 832 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 6 sheets defined 38.2% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.891A pdb=" N ILE B 83 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 41 removed outlier: 3.721A pdb=" N ALA C 37 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TRP C 39 " --> pdb=" O CYS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 65 removed outlier: 3.828A pdb=" N VAL C 52 " --> pdb=" O THR C 48 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU C 65 " --> pdb=" O ALA C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 73 Processing helix chain 'C' and resid 74 through 77 Processing helix chain 'C' and resid 80 through 111 removed outlier: 3.787A pdb=" N LEU C 85 " --> pdb=" O CYS C 81 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE C 86 " --> pdb=" O HIS C 82 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE C 87 " --> pdb=" O GLY C 83 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C 92 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU C 95 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA C 106 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP C 108 " --> pdb=" O ALA C 104 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE C 111 " --> pdb=" O ILE C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 140 removed outlier: 3.879A pdb=" N LYS C 129 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE C 131 " --> pdb=" O ARG C 127 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE C 132 " --> pdb=" O ALA C 128 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N LEU C 138 " --> pdb=" O ILE C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 145 removed outlier: 4.003A pdb=" N THR C 145 " --> pdb=" O ILE C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 188 removed outlier: 3.535A pdb=" N VAL C 185 " --> pdb=" O MET C 181 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N TYR C 186 " --> pdb=" O ASN C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 360 removed outlier: 3.545A pdb=" N VAL C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Proline residue: C 351 - end of helix removed outlier: 4.039A pdb=" N ILE C 355 " --> pdb=" O PRO C 351 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ASN C 356 " --> pdb=" O LEU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 390 removed outlier: 4.155A pdb=" N ASN C 383 " --> pdb=" O LEU C 379 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N SER C 384 " --> pdb=" O SER C 380 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL C 385 " --> pdb=" O HIS C 381 " (cutoff:3.500A) Proline residue: C 388 - end of helix Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 6 removed outlier: 3.659A pdb=" N ARG B 24 " --> pdb=" O THR B 5 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 12 through 13 Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 54 removed outlier: 7.015A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LYS B 49 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE B 33 " --> pdb=" O LYS B 49 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 3 through 6 removed outlier: 3.976A pdb=" N LYS A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A 25 " --> pdb=" O LYS A 3 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 18 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER A 71 " --> pdb=" O TYR A 80 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.596A pdb=" N GLY A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N TRP A 47 " --> pdb=" O LYS A 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.849A pdb=" N CYS A 96 " --> pdb=" O TRP A 115 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N TRP A 115 " --> pdb=" O CYS A 96 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ARG A 98 " --> pdb=" O ASP A 113 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP A 113 " --> pdb=" O ARG A 98 " (cutoff:3.500A) 158 hydrogen bonds defined for protein. 429 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: 0.24 Time building geometry restraints manager: 0.30 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: 998 1.34 - 1.46: 424 1.46 - 1.57: 1549 1.57 - 1.69: 0 1.69 - 1.80: 5 Bond restraints: 2976 Sorted by residual: bond pdb=" CB ASN C 49 " pdb=" CG ASN C 49 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.37e+00 bond pdb=" CA ASN C 49 " pdb=" CB ASN C 49 " ideal model delta sigma weight residual 1.528 1.544 -0.016 1.66e-02 3.63e+03 9.31e-01 bond pdb=" CA ILE C 67 " pdb=" CB ILE C 67 " ideal model delta sigma weight residual 1.539 1.544 -0.005 5.40e-03 3.43e+04 9.20e-01 bond pdb=" CB ASN B 92 " pdb=" CG ASN B 92 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.19e-01 bond pdb=" C GLN C 155 " pdb=" N PRO C 156 " ideal model delta sigma weight residual 1.331 1.343 -0.012 1.27e-02 6.20e+03 8.79e-01 ... (remaining 2971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 3971 1.50 - 3.00: 81 3.00 - 4.49: 12 4.49 - 5.99: 1 5.99 - 7.49: 2 Bond angle restraints: 4067 Sorted by residual: angle pdb=" C LEU C 144 " pdb=" N THR C 145 " pdb=" CA THR C 145 " ideal model delta sigma weight residual 120.58 124.67 -4.09 1.32e+00 5.74e-01 9.60e+00 angle pdb=" CA ASN C 49 " pdb=" CB ASN C 49 " pdb=" CG ASN C 49 " ideal model delta sigma weight residual 112.60 115.03 -2.43 1.00e+00 1.00e+00 5.93e+00 angle pdb=" CB LYS B 103 " pdb=" CG LYS B 103 " pdb=" CD LYS B 103 " ideal model delta sigma weight residual 111.30 116.79 -5.49 2.30e+00 1.89e-01 5.69e+00 angle pdb=" CA LEU A 72 " pdb=" CB LEU A 72 " pdb=" CG LEU A 72 " ideal model delta sigma weight residual 116.30 123.79 -7.49 3.50e+00 8.16e-02 4.58e+00 angle pdb=" CA THR C 145 " pdb=" C THR C 145 " pdb=" N PRO C 146 " ideal model delta sigma weight residual 120.95 118.73 2.22 1.09e+00 8.42e-01 4.15e+00 ... (remaining 4062 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 1542 16.98 - 33.96: 119 33.96 - 50.94: 35 50.94 - 67.92: 4 67.92 - 84.89: 5 Dihedral angle restraints: 1705 sinusoidal: 413 harmonic: 1292 Sorted by residual: dihedral pdb=" CA LEU A 72 " pdb=" C LEU A 72 " pdb=" N GLU A 73 " pdb=" CA GLU A 73 " ideal model delta harmonic sigma weight residual 180.00 162.95 17.05 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CG ARG C 109 " pdb=" CD ARG C 109 " pdb=" NE ARG C 109 " pdb=" CZ ARG C 109 " ideal model delta sinusoidal sigma weight residual 180.00 -136.79 -43.21 2 1.50e+01 4.44e-03 1.00e+01 dihedral pdb=" CA ASP A 90 " pdb=" CB ASP A 90 " pdb=" CG ASP A 90 " pdb=" OD1 ASP A 90 " ideal model delta sinusoidal sigma weight residual -30.00 -82.17 52.17 1 2.00e+01 2.50e-03 9.28e+00 ... (remaining 1702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 257 0.027 - 0.054: 152 0.054 - 0.081: 46 0.081 - 0.108: 25 0.108 - 0.135: 6 Chirality restraints: 486 Sorted by residual: chirality pdb=" CA ASN B 92 " pdb=" N ASN B 92 " pdb=" C ASN B 92 " pdb=" CB ASN B 92 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA ILE A 20 " pdb=" N ILE A 20 " pdb=" C ILE A 20 " pdb=" CB ILE A 20 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 483 not shown) Planarity restraints: 533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 58 " -0.018 5.00e-02 4.00e+02 2.67e-02 1.14e+00 pdb=" N PRO B 59 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO B 59 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 59 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 49 " -0.005 2.00e-02 2.50e+03 9.83e-03 9.66e-01 pdb=" C ASN C 49 " 0.017 2.00e-02 2.50e+03 pdb=" O ASN C 49 " -0.006 2.00e-02 2.50e+03 pdb=" N TYR C 50 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 43 " -0.015 5.00e-02 4.00e+02 2.24e-02 8.04e-01 pdb=" N PRO B 44 " 0.039 5.00e-02 4.00e+02 pdb=" CA PRO B 44 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 44 " -0.012 5.00e-02 4.00e+02 ... (remaining 530 not shown) Histogram of nonbonded interaction distances: 2.52 - 2.99: 1557 2.99 - 3.47: 2825 3.47 - 3.95: 4099 3.95 - 4.42: 4469 4.42 - 4.90: 7494 Nonbonded interactions: 20444 Sorted by model distance: nonbonded pdb=" O ASN C 49 " pdb=" OD1 ASN C 49 " model vdw 2.518 3.040 nonbonded pdb=" N VAL C 171 " pdb=" N ALA C 172 " model vdw 2.596 2.560 nonbonded pdb=" C ASN B 92 " pdb=" OD1 ASN B 92 " model vdw 2.606 3.270 nonbonded pdb=" C SER B 7 " pdb=" OG SER B 7 " model vdw 2.616 2.616 nonbonded pdb=" C SER B 56 " pdb=" OG SER B 56 " model vdw 2.629 2.616 ... (remaining 20439 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: 3.180 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.410 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:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2976 Z= 0.121 Angle : 0.525 7.491 4067 Z= 0.298 Chirality : 0.040 0.135 486 Planarity : 0.003 0.030 533 Dihedral : 14.821 84.894 873 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.00 % Allowed : 36.82 % Favored : 62.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.41), residues: 439 helix: 0.67 (0.43), residues: 140 sheet: -0.04 (0.50), residues: 114 loop : -1.03 (0.48), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 127 TYR 0.008 0.001 TYR B 36 PHE 0.007 0.001 PHE B 21 TRP 0.002 0.001 TRP A 47 HIS 0.001 0.000 HIS C 381 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 2976) covalent geometry : angle 0.52487 ( 4067) hydrogen bonds : bond 0.28478 ( 151) hydrogen bonds : angle 8.22327 ( 429) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.074 Fit side-chains REVERT: B 17 GLU cc_start: 0.8056 (pt0) cc_final: 0.7633 (pt0) REVERT: B 81 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8658 (tm-30) REVERT: B 90 GLN cc_start: 0.9210 (pp30) cc_final: 0.8145 (pp30) REVERT: A 43 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8204 (mm-30) outliers start: 2 outliers final: 2 residues processed: 57 average time/residue: 0.0268 time to fit residues: 2.0883 Evaluate side-chains 56 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain A residue 121 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 0.3980 chunk 16 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- 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 = 0.3633 r_free = 0.3633 target = 0.112105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.086537 restraints weight = 7792.966| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 4.20 r_work: 0.3045 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.056 2976 Z= 0.384 Angle : 0.712 8.408 4067 Z= 0.402 Chirality : 0.046 0.175 486 Planarity : 0.004 0.025 533 Dihedral : 5.190 27.877 473 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 11.94 % Allowed : 24.38 % Favored : 63.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.55 (0.41), residues: 439 helix: 0.80 (0.45), residues: 139 sheet: 0.16 (0.50), residues: 111 loop : -1.58 (0.45), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 127 TYR 0.016 0.002 TYR A 60 PHE 0.019 0.002 PHE C 140 TRP 0.005 0.002 TRP A 50 HIS 0.002 0.001 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00858 ( 2976) covalent geometry : angle 0.71231 ( 4067) hydrogen bonds : bond 0.06556 ( 151) hydrogen bonds : angle 5.67669 ( 429) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 45 time to evaluate : 0.069 Fit side-chains REVERT: B 11 LEU cc_start: 0.8383 (mt) cc_final: 0.8136 (mp) REVERT: B 17 GLU cc_start: 0.7793 (pt0) cc_final: 0.7497 (pt0) REVERT: B 81 GLU cc_start: 0.9429 (mt-10) cc_final: 0.8799 (tm-30) REVERT: B 105 GLU cc_start: 0.7527 (tp30) cc_final: 0.7191 (tp30) REVERT: A 103 TYR cc_start: 0.8736 (t80) cc_final: 0.8476 (t80) outliers start: 24 outliers final: 17 residues processed: 62 average time/residue: 0.0357 time to fit residues: 2.9316 Evaluate side-chains 59 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 122 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 12 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 4 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 6 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 11 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.116504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.090718 restraints weight = 7534.515| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 4.19 r_work: 0.3126 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2976 Z= 0.121 Angle : 0.510 9.373 4067 Z= 0.273 Chirality : 0.042 0.143 486 Planarity : 0.003 0.025 533 Dihedral : 4.191 19.713 473 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 5.47 % Allowed : 29.35 % Favored : 65.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.02 (0.42), residues: 439 helix: 1.17 (0.46), residues: 144 sheet: 0.73 (0.50), residues: 117 loop : -1.49 (0.48), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 109 TYR 0.008 0.001 TYR B 36 PHE 0.010 0.001 PHE C 140 TRP 0.006 0.001 TRP A 47 HIS 0.002 0.001 HIS C 381 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 2976) covalent geometry : angle 0.51003 ( 4067) hydrogen bonds : bond 0.03901 ( 151) hydrogen bonds : angle 4.50597 ( 429) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.130 Fit side-chains REVERT: B 105 GLU cc_start: 0.7541 (tp30) cc_final: 0.7261 (tp30) outliers start: 11 outliers final: 9 residues processed: 58 average time/residue: 0.0532 time to fit residues: 3.9008 Evaluate side-chains 57 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 121 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 22 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 25 optimal weight: 20.0000 overall best weight: 3.0986 ------------------------------------------------------------------------------- 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 = 0.3613 r_free = 0.3613 target = 0.110106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.084868 restraints weight = 7706.642| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 4.12 r_work: 0.3063 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.067 2976 Z= 0.389 Angle : 0.726 8.700 4067 Z= 0.397 Chirality : 0.047 0.180 486 Planarity : 0.004 0.042 533 Dihedral : 5.335 28.985 471 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 11.44 % Allowed : 25.37 % Favored : 63.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.42), residues: 439 helix: 0.78 (0.46), residues: 139 sheet: 0.32 (0.50), residues: 116 loop : -1.79 (0.47), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 109 TYR 0.019 0.002 TYR A 60 PHE 0.021 0.002 PHE C 140 TRP 0.007 0.002 TRP B 94 HIS 0.002 0.001 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00875 ( 2976) covalent geometry : angle 0.72629 ( 4067) hydrogen bonds : bond 0.05274 ( 151) hydrogen bonds : angle 5.24584 ( 429) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 43 time to evaluate : 0.113 Fit side-chains REVERT: B 34 HIS cc_start: 0.9373 (OUTLIER) cc_final: 0.9109 (m-70) REVERT: B 105 GLU cc_start: 0.7493 (tp30) cc_final: 0.7121 (tp30) outliers start: 23 outliers final: 19 residues processed: 58 average time/residue: 0.0662 time to fit residues: 4.6684 Evaluate side-chains 62 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 42 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 122 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 19 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3672 r_free = 0.3672 target = 0.114232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.088656 restraints weight = 7472.301| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 4.15 r_work: 0.3133 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2976 Z= 0.132 Angle : 0.531 9.797 4067 Z= 0.282 Chirality : 0.042 0.144 486 Planarity : 0.003 0.030 533 Dihedral : 4.417 19.478 471 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 9.95 % Allowed : 25.37 % Favored : 64.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.12 (0.43), residues: 439 helix: 1.24 (0.46), residues: 144 sheet: 0.54 (0.50), residues: 117 loop : -1.65 (0.48), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 109 TYR 0.008 0.001 TYR A 60 PHE 0.010 0.001 PHE C 140 TRP 0.007 0.001 TRP A 47 HIS 0.001 0.001 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 2976) covalent geometry : angle 0.53073 ( 4067) hydrogen bonds : bond 0.03550 ( 151) hydrogen bonds : angle 4.46011 ( 429) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 0.112 Fit side-chains REVERT: B 81 GLU cc_start: 0.9374 (mt-10) cc_final: 0.8758 (tm-30) REVERT: B 105 GLU cc_start: 0.7632 (tp30) cc_final: 0.7284 (tp30) outliers start: 20 outliers final: 16 residues processed: 60 average time/residue: 0.0655 time to fit residues: 4.7763 Evaluate side-chains 60 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 121 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 25 optimal weight: 0.3980 chunk 26 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 4 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.115280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.090175 restraints weight = 7412.770| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 4.08 r_work: 0.3140 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2976 Z= 0.135 Angle : 0.522 10.382 4067 Z= 0.275 Chirality : 0.042 0.138 486 Planarity : 0.003 0.034 533 Dihedral : 4.237 19.729 471 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 7.96 % Allowed : 26.87 % Favored : 65.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.09 (0.42), residues: 439 helix: 1.46 (0.46), residues: 147 sheet: 0.70 (0.54), residues: 99 loop : -1.44 (0.46), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 109 TYR 0.008 0.001 TYR A 60 PHE 0.010 0.001 PHE C 140 TRP 0.006 0.001 TRP A 47 HIS 0.001 0.001 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 2976) covalent geometry : angle 0.52213 ( 4067) hydrogen bonds : bond 0.03183 ( 151) hydrogen bonds : angle 4.26735 ( 429) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.067 Fit side-chains REVERT: B 17 GLU cc_start: 0.7960 (pt0) cc_final: 0.7514 (pm20) REVERT: B 105 GLU cc_start: 0.7644 (tp30) cc_final: 0.7265 (tp30) outliers start: 16 outliers final: 14 residues processed: 56 average time/residue: 0.0455 time to fit residues: 3.1916 Evaluate side-chains 56 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 121 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 8 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 chunk 22 optimal weight: 20.0000 chunk 2 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 11 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 30 optimal weight: 20.0000 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.116000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.090905 restraints weight = 7466.285| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 4.08 r_work: 0.3152 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2976 Z= 0.123 Angle : 0.496 7.969 4067 Z= 0.264 Chirality : 0.041 0.137 486 Planarity : 0.003 0.037 533 Dihedral : 4.086 20.704 471 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 8.46 % Allowed : 26.87 % Favored : 64.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.27 (0.43), residues: 439 helix: 1.61 (0.46), residues: 149 sheet: 0.83 (0.54), residues: 99 loop : -1.39 (0.47), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 109 TYR 0.007 0.001 TYR B 36 PHE 0.008 0.001 PHE C 140 TRP 0.007 0.001 TRP A 47 HIS 0.001 0.000 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 2976) covalent geometry : angle 0.49551 ( 4067) hydrogen bonds : bond 0.02950 ( 151) hydrogen bonds : angle 4.12229 ( 429) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.127 Fit side-chains REVERT: B 17 GLU cc_start: 0.7897 (pt0) cc_final: 0.7418 (pm20) REVERT: B 105 GLU cc_start: 0.7665 (tp30) cc_final: 0.7299 (tp30) outliers start: 17 outliers final: 15 residues processed: 59 average time/residue: 0.0580 time to fit residues: 4.2648 Evaluate side-chains 58 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 121 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 16 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 0.0980 chunk 26 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 0.2980 chunk 36 optimal weight: 0.2980 chunk 21 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.5182 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.117415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.092376 restraints weight = 7413.350| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 4.11 r_work: 0.3174 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2976 Z= 0.096 Angle : 0.485 7.407 4067 Z= 0.254 Chirality : 0.041 0.135 486 Planarity : 0.003 0.027 533 Dihedral : 3.868 19.618 471 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 5.47 % Allowed : 30.35 % Favored : 64.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.43), residues: 439 helix: 1.76 (0.46), residues: 149 sheet: 0.94 (0.53), residues: 99 loop : -1.34 (0.47), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 109 TYR 0.006 0.001 TYR A 110 PHE 0.007 0.001 PHE C 140 TRP 0.007 0.001 TRP A 47 HIS 0.001 0.000 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 2976) covalent geometry : angle 0.48452 ( 4067) hydrogen bonds : bond 0.02587 ( 151) hydrogen bonds : angle 3.93877 ( 429) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.114 Fit side-chains REVERT: B 17 GLU cc_start: 0.7977 (pt0) cc_final: 0.7500 (pm20) REVERT: B 105 GLU cc_start: 0.7663 (tp30) cc_final: 0.7289 (tp30) outliers start: 11 outliers final: 10 residues processed: 55 average time/residue: 0.0480 time to fit residues: 3.4369 Evaluate side-chains 55 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 121 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 21 optimal weight: 3.9990 chunk 29 optimal weight: 0.0670 chunk 30 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- 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 = 0.3674 r_free = 0.3674 target = 0.114162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.089061 restraints weight = 7442.816| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 4.02 r_work: 0.3131 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2976 Z= 0.189 Angle : 0.536 6.653 4067 Z= 0.289 Chirality : 0.042 0.142 486 Planarity : 0.003 0.031 533 Dihedral : 4.351 20.633 471 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 6.97 % Allowed : 29.85 % Favored : 63.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.43), residues: 439 helix: 1.68 (0.46), residues: 149 sheet: 0.87 (0.53), residues: 99 loop : -1.39 (0.47), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 109 TYR 0.011 0.001 TYR A 110 PHE 0.012 0.001 PHE C 140 TRP 0.006 0.001 TRP A 47 HIS 0.001 0.000 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 2976) covalent geometry : angle 0.53581 ( 4067) hydrogen bonds : bond 0.03431 ( 151) hydrogen bonds : angle 4.25293 ( 429) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.110 Fit side-chains REVERT: B 17 GLU cc_start: 0.7907 (pt0) cc_final: 0.7400 (pm20) REVERT: B 105 GLU cc_start: 0.7686 (tp30) cc_final: 0.7297 (tp30) outliers start: 14 outliers final: 12 residues processed: 54 average time/residue: 0.0571 time to fit residues: 3.8645 Evaluate side-chains 55 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 121 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 40 optimal weight: 0.0770 chunk 12 optimal weight: 0.2980 chunk 22 optimal weight: 8.9990 chunk 23 optimal weight: 0.0270 chunk 16 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.2800 ------------------------------------------------------------------------------- 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 = 0.3680 r_free = 0.3680 target = 0.114643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.089370 restraints weight = 7629.885| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 4.08 r_work: 0.3131 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2976 Z= 0.170 Angle : 0.530 6.674 4067 Z= 0.286 Chirality : 0.042 0.143 486 Planarity : 0.003 0.027 533 Dihedral : 4.363 20.179 471 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 6.47 % Allowed : 30.85 % Favored : 62.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.23 (0.43), residues: 439 helix: 1.69 (0.46), residues: 147 sheet: 0.71 (0.53), residues: 100 loop : -1.44 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 109 TYR 0.010 0.001 TYR B 36 PHE 0.010 0.001 PHE C 140 TRP 0.006 0.001 TRP A 47 HIS 0.001 0.000 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 2976) covalent geometry : angle 0.52999 ( 4067) hydrogen bonds : bond 0.03300 ( 151) hydrogen bonds : angle 4.25490 ( 429) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.075 Fit side-chains REVERT: B 17 GLU cc_start: 0.7858 (pt0) cc_final: 0.7361 (pm20) REVERT: B 105 GLU cc_start: 0.7712 (tp30) cc_final: 0.7329 (tp30) outliers start: 13 outliers final: 12 residues processed: 53 average time/residue: 0.0309 time to fit residues: 2.1455 Evaluate side-chains 54 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 121 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.111369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.085862 restraints weight = 7786.917| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 4.15 r_work: 0.3041 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 2976 Z= 0.281 Angle : 0.633 10.410 4067 Z= 0.343 Chirality : 0.044 0.170 486 Planarity : 0.004 0.032 533 Dihedral : 4.966 24.513 471 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 7.96 % Allowed : 29.85 % Favored : 62.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.42), residues: 439 helix: 1.51 (0.46), residues: 146 sheet: 0.40 (0.51), residues: 107 loop : -1.65 (0.47), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 109 TYR 0.014 0.002 TYR A 60 PHE 0.015 0.002 PHE C 140 TRP 0.005 0.001 TRP C 136 HIS 0.002 0.001 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00636 ( 2976) covalent geometry : angle 0.63309 ( 4067) hydrogen bonds : bond 0.04215 ( 151) hydrogen bonds : angle 4.69066 ( 429) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 816.28 seconds wall clock time: 14 minutes 40.20 seconds (880.20 seconds total)