Starting phenix.real_space_refine on Wed Sep 17 04:08:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w22_43737/09_2025/8w22_43737.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w22_43737/09_2025/8w22_43737.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8w22_43737/09_2025/8w22_43737.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w22_43737/09_2025/8w22_43737.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w22_43737/09_2025/8w22_43737.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w22_43737/09_2025/8w22_43737.map" } resolution = 4.0 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= 0.072 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 13 5.16 5 C 2333 2.51 5 N 723 2.21 5 O 681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3750 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 685 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 3, 'TRANS': 95} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 7, 'ARG:plan': 1, 'GLU:plan': 5, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "B" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 805 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 117} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLU:plan': 7, 'GLN:plan1': 1, 'ASP:plan': 7, 'ASN:plan1': 4} Unresolved non-hydrogen planarities: 65 Chain: "C" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 2260 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 242} Link IDs: {'PTRANS': 17, 'TRANS': 387} Chain breaks: 12 Unresolved non-hydrogen bonds: 798 Unresolved non-hydrogen angles: 1047 Unresolved non-hydrogen dihedrals: 629 Unresolved non-hydrogen chiralities: 100 Planarities with less than four sites: {'ASP:plan': 37, 'GLN:plan1': 11, 'ASN:plan1': 18, 'ARG:plan': 11, 'GLU:plan': 6, 'HIS:plan': 2, 'TYR:plan': 7, 'PHE:plan': 3, 'TRP:plan': 7} Unresolved non-hydrogen planarities: 428 Time building chain proxies: 1.25, per 1000 atoms: 0.33 Number of scatterers: 3750 At special positions: 0 Unit cell: (69.126, 131.508, 116.334, 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 13 16.00 O 681 8.00 N 723 7.00 C 2333 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 78 " - pdb=" SG CYS B 96 " distance=2.05 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 71 " distance=2.08 Simple disulfide: pdb=" SG CYS C 192 " - pdb=" SG CYS C 222 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.34 Conformation dependent library (CDL) restraints added in 201.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1122 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 9 sheets defined 19.4% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 99 through 111 removed outlier: 3.577A pdb=" N MET A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 123 removed outlier: 3.959A pdb=" N ASP A 121 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 134 Processing helix chain 'A' and resid 136 through 139 Processing helix chain 'A' and resid 140 through 145 Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 158 through 170 Processing helix chain 'A' and resid 172 through 180 Processing helix chain 'A' and resid 182 through 197 Processing helix chain 'B' and resid 54 through 62 removed outlier: 3.504A pdb=" N ALA B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 151 Processing helix chain 'C' and resid 69 through 73 Processing helix chain 'C' and resid 238 through 247 Processing sheet with id=AA1, first strand: chain 'B' and resid 73 through 76 removed outlier: 3.711A pdb=" N CYS B 96 " --> pdb=" O THR B 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 104 through 106 removed outlier: 3.525A pdb=" N ALA B 104 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR B 126 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LEU B 162 " --> pdb=" O LYS B 124 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS B 124 " --> pdb=" O LEU B 162 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 43 through 48 removed outlier: 3.536A pdb=" N GLU C 112 " --> pdb=" O ARG C 125 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N THR C 91 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 137 through 138 removed outlier: 7.338A pdb=" N ARG C 137 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N GLY C 212 " --> pdb=" O ARG C 137 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE C 233 " --> pdb=" O ASN C 215 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N SER C 217 " --> pdb=" O ASP C 231 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ASP C 231 " --> pdb=" O SER C 217 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N THR C 184 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N VAL C 173 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASP C 203 " --> pdb=" O PRO C 148 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL C 152 " --> pdb=" O PRO C 199 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY C 212 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLN C 202 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU C 210 " --> pdb=" O GLN C 202 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LYS C 204 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU C 208 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 259 through 262 Processing sheet with id=AA6, first strand: chain 'C' and resid 333 through 334 Processing sheet with id=AA7, first strand: chain 'C' and resid 369 through 369 Processing sheet with id=AA8, first strand: chain 'C' and resid 409 through 413 removed outlier: 3.529A pdb=" N THR C 411 " --> pdb=" O THR C 425 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N THR C 425 " --> pdb=" O THR C 411 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 485 through 486 173 hydrogen bonds defined for protein. 453 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: 0.59 Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1142 1.33 - 1.45: 504 1.45 - 1.58: 2130 1.58 - 1.70: 0 1.70 - 1.82: 20 Bond restraints: 3796 Sorted by residual: bond pdb=" NE ARG A 106 " pdb=" CZ ARG A 106 " ideal model delta sigma weight residual 1.326 1.355 -0.029 1.10e-02 8.26e+03 6.76e+00 bond pdb=" NE ARG C 119 " pdb=" CZ ARG C 119 " ideal model delta sigma weight residual 1.326 1.353 -0.027 1.10e-02 8.26e+03 6.04e+00 bond pdb=" NE ARG A 162 " pdb=" CZ ARG A 162 " ideal model delta sigma weight residual 1.326 1.351 -0.025 1.10e-02 8.26e+03 5.31e+00 bond pdb=" NE ARG C 97 " pdb=" CZ ARG C 97 " ideal model delta sigma weight residual 1.326 1.351 -0.025 1.10e-02 8.26e+03 5.20e+00 bond pdb=" NE ARG A 124 " pdb=" CZ ARG A 124 " ideal model delta sigma weight residual 1.326 1.351 -0.025 1.10e-02 8.26e+03 5.05e+00 ... (remaining 3791 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 4429 1.58 - 3.16: 651 3.16 - 4.75: 60 4.75 - 6.33: 27 6.33 - 7.91: 28 Bond angle restraints: 5195 Sorted by residual: angle pdb=" C VAL C 114 " pdb=" N PRO C 115 " pdb=" CA PRO C 115 " ideal model delta sigma weight residual 119.85 127.71 -7.86 1.01e+00 9.80e-01 6.05e+01 angle pdb=" C ASP B 121 " pdb=" N PRO B 122 " pdb=" CA PRO B 122 " ideal model delta sigma weight residual 119.76 126.92 -7.16 1.03e+00 9.43e-01 4.84e+01 angle pdb=" C ARG C 502 " pdb=" N PRO C 503 " pdb=" CA PRO C 503 " ideal model delta sigma weight residual 120.03 126.91 -6.88 9.90e-01 1.02e+00 4.83e+01 angle pdb=" C GLY A 158 " pdb=" N PRO A 159 " pdb=" CA PRO A 159 " ideal model delta sigma weight residual 119.32 127.23 -7.91 1.14e+00 7.69e-01 4.81e+01 angle pdb=" C MET B 43 " pdb=" N PRO B 44 " pdb=" CA PRO B 44 " ideal model delta sigma weight residual 120.31 127.11 -6.80 9.80e-01 1.04e+00 4.81e+01 ... (remaining 5190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.31: 2128 12.31 - 24.61: 57 24.61 - 36.92: 16 36.92 - 49.23: 6 49.23 - 61.53: 6 Dihedral angle restraints: 2213 sinusoidal: 467 harmonic: 1746 Sorted by residual: dihedral pdb=" CB CYS C 192 " pdb=" SG CYS C 192 " pdb=" SG CYS C 222 " pdb=" CB CYS C 222 " ideal model delta sinusoidal sigma weight residual 93.00 154.53 -61.53 1 1.00e+01 1.00e-02 5.02e+01 dihedral pdb=" CB CYS C 55 " pdb=" SG CYS C 55 " pdb=" SG CYS C 71 " pdb=" CB CYS C 71 " ideal model delta sinusoidal sigma weight residual 93.00 137.06 -44.06 1 1.00e+01 1.00e-02 2.70e+01 dihedral pdb=" CB CYS B 78 " pdb=" SG CYS B 78 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 120.80 -27.80 1 1.00e+01 1.00e-02 1.11e+01 ... (remaining 2210 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 349 0.039 - 0.079: 170 0.079 - 0.118: 73 0.118 - 0.157: 24 0.157 - 0.197: 3 Chirality restraints: 619 Sorted by residual: chirality pdb=" CA ILE C 191 " pdb=" N ILE C 191 " pdb=" C ILE C 191 " pdb=" CB ILE C 191 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.66e-01 chirality pdb=" CA ILE C 130 " pdb=" N ILE C 130 " pdb=" C ILE C 130 " pdb=" CB ILE C 130 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.54e-01 chirality pdb=" CG LEU C 46 " pdb=" CB LEU C 46 " pdb=" CD1 LEU C 46 " pdb=" CD2 LEU C 46 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.70e-01 ... (remaining 616 not shown) Planarity restraints: 718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 52 " -0.028 2.00e-02 2.50e+03 1.43e-02 4.08e+00 pdb=" CG TYR B 52 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR B 52 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR B 52 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR B 52 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 52 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 52 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 52 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 199 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.34e+00 pdb=" C PRO C 199 " 0.032 2.00e-02 2.50e+03 pdb=" O PRO C 199 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU C 200 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 52 " 0.021 2.00e-02 2.50e+03 1.11e-02 2.48e+00 pdb=" CG TYR C 52 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR C 52 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR C 52 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR C 52 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR C 52 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 52 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 52 " 0.015 2.00e-02 2.50e+03 ... (remaining 715 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 1763 2.98 - 3.46: 3227 3.46 - 3.94: 5318 3.94 - 4.42: 5604 4.42 - 4.90: 9568 Nonbonded interactions: 25480 Sorted by model distance: nonbonded pdb=" O TYR B 147 " pdb=" C GLY B 148 " model vdw 2.497 3.270 nonbonded pdb=" O TYR B 147 " pdb=" N ALA B 150 " model vdw 2.511 3.120 nonbonded pdb=" N GLY C 194 " pdb=" N ASP C 195 " model vdw 2.565 2.560 nonbonded pdb=" N LYS C 39 " pdb=" N LEU C 40 " model vdw 2.578 2.560 nonbonded pdb=" N GLY C 268 " pdb=" N ARG C 269 " model vdw 2.602 2.560 ... (remaining 25475 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 group one per residue 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: 2.700 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: 0.020 Set scattering table: 0.010 Process input model: 6.310 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 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 : 0.008 0.051 3799 Z= 0.495 Angle : 1.269 7.910 5201 Z= 0.883 Chirality : 0.055 0.197 619 Planarity : 0.005 0.018 718 Dihedral : 7.997 59.354 1082 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.84 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.30 (0.35), residues: 599 helix: -0.58 (0.43), residues: 110 sheet: 1.43 (0.46), residues: 140 loop : 0.03 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 53 TYR 0.028 0.004 TYR B 52 PHE 0.018 0.003 PHE C 171 TRP 0.014 0.004 TRP C 64 HIS 0.004 0.001 HIS C 116 Details of bonding type rmsd covalent geometry : bond 0.00810 ( 3796) covalent geometry : angle 1.26640 ( 5195) SS BOND : bond 0.03142 ( 3) SS BOND : angle 2.84746 ( 6) hydrogen bonds : bond 0.20361 ( 173) hydrogen bonds : angle 8.01423 ( 453) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.147 Fit side-chains REVERT: A 106 ARG cc_start: 0.6014 (ttm110) cc_final: 0.5118 (tpp-160) REVERT: A 170 GLN cc_start: 0.8282 (mt0) cc_final: 0.8030 (mt0) REVERT: B 100 MET cc_start: 0.8401 (mmm) cc_final: 0.7447 (mpp) REVERT: C 125 ARG cc_start: 0.7762 (ttt180) cc_final: 0.7217 (tmt-80) REVERT: C 137 ARG cc_start: 0.7417 (mtp180) cc_final: 0.7137 (mtp85) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0966 time to fit residues: 8.2832 Evaluate side-chains 41 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.148544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.118847 restraints weight = 7326.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.116903 restraints weight = 6629.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.117898 restraints weight = 5504.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.118147 restraints weight = 4429.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.120261 restraints weight = 3800.328| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 3799 Z= 0.235 Angle : 0.672 6.481 5201 Z= 0.367 Chirality : 0.048 0.170 619 Planarity : 0.005 0.029 718 Dihedral : 4.586 19.774 644 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.89 % Allowed : 15.00 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.64 (0.36), residues: 599 helix: 0.63 (0.49), residues: 116 sheet: 1.04 (0.44), residues: 160 loop : 0.13 (0.37), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 193 TYR 0.019 0.002 TYR A 185 PHE 0.017 0.003 PHE C 171 TRP 0.027 0.003 TRP B 117 HIS 0.003 0.001 HIS C 116 Details of bonding type rmsd covalent geometry : bond 0.00509 ( 3796) covalent geometry : angle 0.67037 ( 5195) SS BOND : bond 0.01416 ( 3) SS BOND : angle 1.62222 ( 6) hydrogen bonds : bond 0.05047 ( 173) hydrogen bonds : angle 5.56057 ( 453) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.147 Fit side-chains REVERT: A 106 ARG cc_start: 0.5631 (ttm110) cc_final: 0.4819 (tpp-160) REVERT: A 156 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8430 (tt) REVERT: B 58 ILE cc_start: 0.8949 (mm) cc_final: 0.8662 (mm) REVERT: B 100 MET cc_start: 0.9032 (mmm) cc_final: 0.8802 (mmt) REVERT: C 125 ARG cc_start: 0.7911 (ttt180) cc_final: 0.7683 (ttt90) REVERT: C 137 ARG cc_start: 0.7796 (mtp180) cc_final: 0.7216 (mtp85) outliers start: 7 outliers final: 4 residues processed: 47 average time/residue: 0.0671 time to fit residues: 4.1364 Evaluate side-chains 45 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 137 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 9 optimal weight: 1.9990 chunk 52 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 21 optimal weight: 0.2980 chunk 16 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 GLN C 167 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.149239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.116962 restraints weight = 7190.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.119352 restraints weight = 4658.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.120714 restraints weight = 3325.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.122067 restraints weight = 2596.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.122825 restraints weight = 2133.326| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3799 Z= 0.166 Angle : 0.545 5.964 5201 Z= 0.293 Chirality : 0.045 0.138 619 Planarity : 0.004 0.033 718 Dihedral : 3.976 16.780 644 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 5.00 % Allowed : 17.22 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.59 (0.36), residues: 599 helix: 1.15 (0.53), residues: 110 sheet: 0.72 (0.42), residues: 167 loop : 0.04 (0.37), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 116 TYR 0.010 0.001 TYR A 185 PHE 0.015 0.002 PHE C 171 TRP 0.025 0.002 TRP B 117 HIS 0.003 0.001 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 3796) covalent geometry : angle 0.54422 ( 5195) SS BOND : bond 0.00506 ( 3) SS BOND : angle 1.21980 ( 6) hydrogen bonds : bond 0.04333 ( 173) hydrogen bonds : angle 4.99733 ( 453) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.145 Fit side-chains REVERT: B 100 MET cc_start: 0.9063 (mmm) cc_final: 0.8666 (mmm) REVERT: C 125 ARG cc_start: 0.7747 (ttt180) cc_final: 0.7485 (ttt90) REVERT: C 137 ARG cc_start: 0.7915 (mtp180) cc_final: 0.7211 (mtp85) outliers start: 9 outliers final: 5 residues processed: 48 average time/residue: 0.0557 time to fit residues: 3.5851 Evaluate side-chains 44 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 164 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 34 optimal weight: 0.0470 chunk 49 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 37 optimal weight: 0.3980 chunk 56 optimal weight: 0.6980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.150154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.122226 restraints weight = 7168.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.122267 restraints weight = 5805.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.123170 restraints weight = 5344.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.123184 restraints weight = 3817.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.123229 restraints weight = 3903.481| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3799 Z= 0.133 Angle : 0.514 5.370 5201 Z= 0.273 Chirality : 0.045 0.132 619 Planarity : 0.004 0.037 718 Dihedral : 3.781 14.671 644 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.89 % Allowed : 16.11 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.55 (0.37), residues: 599 helix: 1.21 (0.53), residues: 110 sheet: 0.60 (0.44), residues: 161 loop : 0.04 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 193 TYR 0.007 0.001 TYR A 185 PHE 0.015 0.002 PHE C 171 TRP 0.018 0.002 TRP B 117 HIS 0.003 0.001 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 3796) covalent geometry : angle 0.50980 ( 5195) SS BOND : bond 0.00289 ( 3) SS BOND : angle 1.98354 ( 6) hydrogen bonds : bond 0.03739 ( 173) hydrogen bonds : angle 4.84820 ( 453) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.152 Fit side-chains REVERT: A 125 LEU cc_start: 0.7947 (tp) cc_final: 0.7700 (tt) REVERT: C 125 ARG cc_start: 0.7995 (ttt180) cc_final: 0.7711 (ttt90) REVERT: C 137 ARG cc_start: 0.8047 (mtp180) cc_final: 0.7344 (mtp85) outliers start: 7 outliers final: 6 residues processed: 48 average time/residue: 0.0568 time to fit residues: 3.6630 Evaluate side-chains 48 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 164 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 24 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 51 optimal weight: 0.0270 chunk 54 optimal weight: 9.9990 chunk 37 optimal weight: 0.2980 chunk 35 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 chunk 47 optimal weight: 6.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- 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 = 0.3908 r_free = 0.3908 target = 0.151388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.123229 restraints weight = 7049.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.120665 restraints weight = 5615.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.122104 restraints weight = 4280.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.122355 restraints weight = 3635.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.122660 restraints weight = 3160.496| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3799 Z= 0.115 Angle : 0.484 5.395 5201 Z= 0.255 Chirality : 0.044 0.128 619 Planarity : 0.003 0.040 718 Dihedral : 3.489 13.526 644 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.44 % Allowed : 17.22 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.61 (0.37), residues: 599 helix: 1.29 (0.54), residues: 110 sheet: 0.53 (0.43), residues: 161 loop : 0.14 (0.38), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 68 TYR 0.006 0.001 TYR A 185 PHE 0.015 0.002 PHE C 171 TRP 0.016 0.002 TRP B 117 HIS 0.003 0.001 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 3796) covalent geometry : angle 0.48311 ( 5195) SS BOND : bond 0.00244 ( 3) SS BOND : angle 1.05247 ( 6) hydrogen bonds : bond 0.03443 ( 173) hydrogen bonds : angle 4.65251 ( 453) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.166 Fit side-chains REVERT: A 107 MET cc_start: 0.7721 (mtm) cc_final: 0.7465 (mtm) REVERT: A 125 LEU cc_start: 0.7953 (tp) cc_final: 0.7674 (tt) REVERT: C 125 ARG cc_start: 0.7977 (ttt180) cc_final: 0.7683 (ttt90) REVERT: C 137 ARG cc_start: 0.8051 (mtp180) cc_final: 0.7247 (mtp85) outliers start: 8 outliers final: 6 residues processed: 50 average time/residue: 0.0528 time to fit residues: 3.5966 Evaluate side-chains 46 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 164 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 49 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 40 optimal weight: 0.0070 chunk 29 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 = 0.3838 r_free = 0.3838 target = 0.145942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.118497 restraints weight = 7343.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.117154 restraints weight = 5729.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.118481 restraints weight = 5866.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.118957 restraints weight = 3959.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.118724 restraints weight = 3882.236| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.4988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3799 Z= 0.154 Angle : 0.518 5.175 5201 Z= 0.277 Chirality : 0.045 0.135 619 Planarity : 0.004 0.039 718 Dihedral : 3.778 15.757 644 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 6.11 % Allowed : 17.78 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.54 (0.37), residues: 599 helix: 1.16 (0.55), residues: 109 sheet: 0.56 (0.43), residues: 154 loop : 0.09 (0.38), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 156 TYR 0.009 0.001 TYR A 185 PHE 0.013 0.002 PHE C 171 TRP 0.017 0.002 TRP B 117 HIS 0.004 0.002 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 3796) covalent geometry : angle 0.51705 ( 5195) SS BOND : bond 0.00377 ( 3) SS BOND : angle 1.16771 ( 6) hydrogen bonds : bond 0.03962 ( 173) hydrogen bonds : angle 4.97840 ( 453) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.130 Fit side-chains REVERT: C 125 ARG cc_start: 0.8133 (ttt180) cc_final: 0.7831 (ttt90) REVERT: C 137 ARG cc_start: 0.8210 (mtp180) cc_final: 0.7382 (mtp85) outliers start: 11 outliers final: 8 residues processed: 49 average time/residue: 0.0609 time to fit residues: 4.0125 Evaluate side-chains 45 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 164 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 1 optimal weight: 0.2980 chunk 52 optimal weight: 20.0000 chunk 30 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 51 optimal weight: 0.0970 chunk 39 optimal weight: 0.4980 chunk 29 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 23 optimal weight: 0.0030 chunk 37 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 overall best weight: 0.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.149533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.120840 restraints weight = 7444.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.119668 restraints weight = 6190.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.120898 restraints weight = 4724.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.121138 restraints weight = 3971.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.121524 restraints weight = 3357.035| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3799 Z= 0.096 Angle : 0.484 7.813 5201 Z= 0.245 Chirality : 0.044 0.128 619 Planarity : 0.003 0.044 718 Dihedral : 3.340 13.409 644 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.44 % Allowed : 18.89 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.63 (0.37), residues: 599 helix: 1.29 (0.55), residues: 109 sheet: 0.65 (0.46), residues: 134 loop : 0.14 (0.36), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 193 TYR 0.006 0.001 TYR A 138 PHE 0.014 0.001 PHE C 171 TRP 0.008 0.001 TRP B 117 HIS 0.002 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 3796) covalent geometry : angle 0.48399 ( 5195) SS BOND : bond 0.00233 ( 3) SS BOND : angle 0.62245 ( 6) hydrogen bonds : bond 0.03044 ( 173) hydrogen bonds : angle 4.59431 ( 453) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.137 Fit side-chains REVERT: A 170 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7801 (mm110) REVERT: C 125 ARG cc_start: 0.8099 (ttt180) cc_final: 0.7795 (ttt90) REVERT: C 137 ARG cc_start: 0.8099 (mtp180) cc_final: 0.7246 (mtp85) outliers start: 8 outliers final: 6 residues processed: 46 average time/residue: 0.0544 time to fit residues: 3.4170 Evaluate side-chains 45 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 164 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 19 optimal weight: 0.0970 chunk 41 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 1 optimal weight: 0.1980 chunk 5 optimal weight: 0.1980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.148930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.120572 restraints weight = 7294.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.118750 restraints weight = 6114.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.119906 restraints weight = 4804.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.120306 restraints weight = 3891.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.120581 restraints weight = 3511.148| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3799 Z= 0.104 Angle : 0.484 7.224 5201 Z= 0.245 Chirality : 0.044 0.128 619 Planarity : 0.003 0.044 718 Dihedral : 3.300 14.062 644 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 5.56 % Allowed : 17.78 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.66 (0.37), residues: 599 helix: 1.29 (0.55), residues: 109 sheet: 0.64 (0.46), residues: 133 loop : 0.18 (0.37), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 193 TYR 0.005 0.001 TYR A 138 PHE 0.014 0.001 PHE C 171 TRP 0.012 0.001 TRP B 117 HIS 0.003 0.001 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 3796) covalent geometry : angle 0.48381 ( 5195) SS BOND : bond 0.00234 ( 3) SS BOND : angle 0.64588 ( 6) hydrogen bonds : bond 0.03067 ( 173) hydrogen bonds : angle 4.58565 ( 453) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.148 Fit side-chains REVERT: A 170 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7561 (mm110) REVERT: B 112 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8438 (mp10) REVERT: C 125 ARG cc_start: 0.8106 (ttt180) cc_final: 0.7807 (ttt90) REVERT: C 137 ARG cc_start: 0.8127 (mtp180) cc_final: 0.7265 (mtp85) outliers start: 10 outliers final: 8 residues processed: 45 average time/residue: 0.0627 time to fit residues: 3.7727 Evaluate side-chains 48 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 164 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 57 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 37 optimal weight: 0.0770 chunk 27 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 4 optimal weight: 0.1980 chunk 32 optimal weight: 0.0770 chunk 39 optimal weight: 0.9980 chunk 55 optimal weight: 8.9990 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.148862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.120544 restraints weight = 7310.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.118491 restraints weight = 6780.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.119830 restraints weight = 5228.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.120378 restraints weight = 4001.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.120724 restraints weight = 3648.619| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3799 Z= 0.099 Angle : 0.483 7.259 5201 Z= 0.244 Chirality : 0.043 0.127 619 Planarity : 0.003 0.044 718 Dihedral : 3.260 13.326 644 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 5.56 % Allowed : 19.44 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.65 (0.37), residues: 599 helix: 1.29 (0.55), residues: 109 sheet: 0.61 (0.46), residues: 133 loop : 0.18 (0.37), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 193 TYR 0.005 0.001 TYR A 138 PHE 0.016 0.001 PHE C 171 TRP 0.015 0.001 TRP B 117 HIS 0.002 0.001 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 3796) covalent geometry : angle 0.48274 ( 5195) SS BOND : bond 0.00242 ( 3) SS BOND : angle 0.71674 ( 6) hydrogen bonds : bond 0.02984 ( 173) hydrogen bonds : angle 4.54502 ( 453) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.124 Fit side-chains REVERT: B 112 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8437 (mp10) REVERT: C 125 ARG cc_start: 0.8165 (ttt180) cc_final: 0.7904 (ttt90) REVERT: C 137 ARG cc_start: 0.8158 (mtp180) cc_final: 0.7305 (mtp85) outliers start: 10 outliers final: 7 residues processed: 46 average time/residue: 0.0576 time to fit residues: 3.5619 Evaluate side-chains 44 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 164 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 52 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 58 optimal weight: 0.0980 chunk 16 optimal weight: 0.2980 chunk 29 optimal weight: 0.0980 chunk 38 optimal weight: 0.0070 chunk 37 optimal weight: 0.1980 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 0.3980 chunk 59 optimal weight: 3.9990 overall best weight: 0.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.152171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.124265 restraints weight = 7357.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.122180 restraints weight = 6631.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.123405 restraints weight = 5283.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.123947 restraints weight = 4030.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.124293 restraints weight = 3650.317| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3799 Z= 0.074 Angle : 0.464 8.000 5201 Z= 0.231 Chirality : 0.043 0.125 619 Planarity : 0.003 0.046 718 Dihedral : 3.026 11.846 644 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.78 % Allowed : 21.67 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.86 (0.37), residues: 599 helix: 1.44 (0.55), residues: 110 sheet: 0.71 (0.44), residues: 145 loop : 0.33 (0.38), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 193 TYR 0.007 0.001 TYR A 138 PHE 0.020 0.001 PHE C 171 TRP 0.008 0.001 TRP B 117 HIS 0.001 0.000 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00165 ( 3796) covalent geometry : angle 0.46369 ( 5195) SS BOND : bond 0.00179 ( 3) SS BOND : angle 0.52497 ( 6) hydrogen bonds : bond 0.02373 ( 173) hydrogen bonds : angle 4.26882 ( 453) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.153 Fit side-chains REVERT: C 125 ARG cc_start: 0.7981 (ttt180) cc_final: 0.7739 (ttt90) REVERT: C 137 ARG cc_start: 0.8112 (mtp180) cc_final: 0.7283 (mtp85) outliers start: 5 outliers final: 5 residues processed: 44 average time/residue: 0.0559 time to fit residues: 3.3075 Evaluate side-chains 44 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 164 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 45 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 10 optimal weight: 0.0870 chunk 39 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 56 optimal weight: 7.9990 chunk 40 optimal weight: 0.0970 chunk 7 optimal weight: 0.8980 chunk 38 optimal weight: 0.2980 chunk 14 optimal weight: 0.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- 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 = 0.3870 r_free = 0.3870 target = 0.148656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.120388 restraints weight = 7168.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.118384 restraints weight = 6486.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.119294 restraints weight = 5204.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.119848 restraints weight = 4228.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.120401 restraints weight = 3678.744| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.5413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3799 Z= 0.111 Angle : 0.493 7.098 5201 Z= 0.248 Chirality : 0.043 0.125 619 Planarity : 0.003 0.043 718 Dihedral : 3.201 12.584 644 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.78 % Allowed : 23.33 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.72 (0.37), residues: 599 helix: 1.16 (0.54), residues: 116 sheet: 0.68 (0.45), residues: 143 loop : 0.25 (0.38), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 193 TYR 0.005 0.001 TYR A 185 PHE 0.013 0.001 PHE C 171 TRP 0.007 0.001 TRP B 117 HIS 0.003 0.001 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 3796) covalent geometry : angle 0.49230 ( 5195) SS BOND : bond 0.00229 ( 3) SS BOND : angle 0.91940 ( 6) hydrogen bonds : bond 0.03061 ( 173) hydrogen bonds : angle 4.47210 ( 453) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 906.03 seconds wall clock time: 16 minutes 13.07 seconds (973.07 seconds total)