Starting phenix.real_space_refine on Fri May 9 23:37:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jh1_61469/05_2025/9jh1_61469.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jh1_61469/05_2025/9jh1_61469.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jh1_61469/05_2025/9jh1_61469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jh1_61469/05_2025/9jh1_61469.map" model { file = "/net/cci-nas-00/data/ceres_data/9jh1_61469/05_2025/9jh1_61469.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jh1_61469/05_2025/9jh1_61469.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.042 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: 5 Type Number sf(0) Gaussians K 2 8.98 5 S 32 5.16 5 C 2799 2.51 5 N 705 2.21 5 O 717 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 4255 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2095 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain breaks: 1 Chain: "B" Number of atoms: 2102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2102 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 6, 'TRANS': 256} Chain breaks: 1 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, 'EIC': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-2': 1, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, 'EIC': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-2': 1, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 3.38, per 1000 atoms: 0.79 Number of scatterers: 4255 At special positions: 0 Unit cell: (68.036, 88.54, 95.064, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 2 19.00 S 32 16.00 O 717 8.00 N 705 7.00 C 2799 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: 1.28 Conformation dependent library (CDL) restraints added in 502.1 milliseconds 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 970 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 81.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 20 through 22 No H-bonds generated for 'chain 'A' and resid 20 through 22' Processing helix chain 'A' and resid 23 through 63 removed outlier: 3.582A pdb=" N GLU A 42 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N HIS A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 84 Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 120 through 167 Proline residue: A 136 - end of helix Processing helix chain 'A' and resid 193 through 221 Proline residue: A 218 - end of helix Processing helix chain 'A' and resid 223 through 236 Processing helix chain 'A' and resid 253 through 298 Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 23 through 63 removed outlier: 3.582A pdb=" N GLU B 42 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ALA B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N HIS B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 84 Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 120 through 167 Proline residue: B 136 - end of helix Processing helix chain 'B' and resid 193 through 221 Proline residue: B 218 - end of helix Processing helix chain 'B' and resid 223 through 236 Processing helix chain 'B' and resid 253 through 298 346 hydrogen bonds defined for protein. 1038 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.11 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1303 1.34 - 1.46: 1024 1.46 - 1.58: 1985 1.58 - 1.69: 0 1.69 - 1.81: 44 Bond restraints: 4356 Sorted by residual: bond pdb=" C10 EIC A 402 " pdb=" C9 EIC A 402 " ideal model delta sigma weight residual 1.332 1.528 -0.196 2.00e-02 2.50e+03 9.57e+01 bond pdb=" C12 EIC A 402 " pdb=" C13 EIC A 402 " ideal model delta sigma weight residual 1.332 1.527 -0.195 2.00e-02 2.50e+03 9.55e+01 bond pdb=" C12 EIC B 402 " pdb=" C13 EIC B 402 " ideal model delta sigma weight residual 1.332 1.527 -0.195 2.00e-02 2.50e+03 9.53e+01 bond pdb=" C10 EIC B 402 " pdb=" C9 EIC B 402 " ideal model delta sigma weight residual 1.332 1.527 -0.195 2.00e-02 2.50e+03 9.46e+01 bond pdb=" C31 POV A 401 " pdb=" O31 POV A 401 " ideal model delta sigma weight residual 1.327 1.261 0.066 2.00e-02 2.50e+03 1.08e+01 ... (remaining 4351 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 5748 3.18 - 6.35: 100 6.35 - 9.53: 11 9.53 - 12.70: 7 12.70 - 15.88: 8 Bond angle restraints: 5874 Sorted by residual: angle pdb=" C12 EIC A 402 " pdb=" C13 EIC A 402 " pdb=" C14 EIC A 402 " ideal model delta sigma weight residual 128.16 112.28 15.88 3.00e+00 1.11e-01 2.80e+01 angle pdb=" C12 EIC B 402 " pdb=" C13 EIC B 402 " pdb=" C14 EIC B 402 " ideal model delta sigma weight residual 128.16 112.28 15.88 3.00e+00 1.11e-01 2.80e+01 angle pdb=" C10 EIC A 402 " pdb=" C9 EIC A 402 " pdb=" C8 EIC A 402 " ideal model delta sigma weight residual 127.75 112.16 15.59 3.00e+00 1.11e-01 2.70e+01 angle pdb=" C10 EIC B 402 " pdb=" C9 EIC B 402 " pdb=" C8 EIC B 402 " ideal model delta sigma weight residual 127.75 112.23 15.52 3.00e+00 1.11e-01 2.68e+01 angle pdb=" C11 EIC B 402 " pdb=" C12 EIC B 402 " pdb=" C13 EIC B 402 " ideal model delta sigma weight residual 127.66 112.40 15.26 3.00e+00 1.11e-01 2.59e+01 ... (remaining 5869 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.80: 2134 19.80 - 39.60: 306 39.60 - 59.40: 54 59.40 - 79.20: 10 79.20 - 98.99: 8 Dihedral angle restraints: 2512 sinusoidal: 995 harmonic: 1517 Sorted by residual: dihedral pdb=" CA ARG B 87 " pdb=" C ARG B 87 " pdb=" N VAL B 88 " pdb=" CA VAL B 88 " ideal model delta harmonic sigma weight residual -180.00 -156.83 -23.17 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA ARG A 87 " pdb=" C ARG A 87 " pdb=" N VAL A 88 " pdb=" CA VAL A 88 " ideal model delta harmonic sigma weight residual -180.00 -156.86 -23.14 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA ARG B 92 " pdb=" C ARG B 92 " pdb=" N PRO B 93 " pdb=" CA PRO B 93 " ideal model delta harmonic sigma weight residual 180.00 160.83 19.17 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 2509 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 487 0.043 - 0.087: 122 0.087 - 0.130: 26 0.130 - 0.174: 6 0.174 - 0.217: 4 Chirality restraints: 645 Sorted by residual: chirality pdb=" CA GLU B 42 " pdb=" N GLU B 42 " pdb=" C GLU B 42 " pdb=" CB GLU B 42 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA GLU A 42 " pdb=" N GLU A 42 " pdb=" C GLU A 42 " pdb=" CB GLU A 42 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB ILE B 283 " pdb=" CA ILE B 283 " pdb=" CG1 ILE B 283 " pdb=" CG2 ILE B 283 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.55e-01 ... (remaining 642 not shown) Planarity restraints: 728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 EIC A 402 " -0.355 2.00e-02 2.50e+03 3.43e-01 1.18e+03 pdb=" C12 EIC A 402 " 0.383 2.00e-02 2.50e+03 pdb=" C13 EIC A 402 " 0.300 2.00e-02 2.50e+03 pdb=" C14 EIC A 402 " -0.328 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 EIC B 402 " 0.352 2.00e-02 2.50e+03 3.43e-01 1.17e+03 pdb=" C12 EIC B 402 " -0.373 2.00e-02 2.50e+03 pdb=" C13 EIC B 402 " -0.311 2.00e-02 2.50e+03 pdb=" C14 EIC B 402 " 0.332 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 EIC A 402 " 0.439 2.00e-02 2.50e+03 3.29e-01 1.08e+03 pdb=" C11 EIC A 402 " -0.158 2.00e-02 2.50e+03 pdb=" C8 EIC A 402 " 0.156 2.00e-02 2.50e+03 pdb=" C9 EIC A 402 " -0.437 2.00e-02 2.50e+03 ... (remaining 725 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.71: 189 2.71 - 3.32: 5444 3.32 - 3.93: 8454 3.93 - 4.53: 10968 4.53 - 5.14: 16369 Nonbonded interactions: 41424 Sorted by model distance: nonbonded pdb=" OE2 GLU A 220 " pdb=" OH TYR A 257 " model vdw 2.104 3.040 nonbonded pdb=" OE2 GLU B 220 " pdb=" OH TYR B 257 " model vdw 2.104 3.040 nonbonded pdb=" CG2 THR A 237 " pdb=" K K A 403 " model vdw 2.220 3.270 nonbonded pdb=" CG2 THR B 237 " pdb=" K K A 403 " model vdw 2.236 3.270 nonbonded pdb=" OD1 ASP A 89 " pdb=" NH2 ARG B 72 " model vdw 2.250 3.120 ... (remaining 41419 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 18 through 299 or resid 401 through 403)) } 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.260 Find NCS groups from input model: 0.150 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 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 0.196 4356 Z= 0.383 Angle : 1.141 15.879 5874 Z= 0.526 Chirality : 0.043 0.217 645 Planarity : 0.027 0.343 728 Dihedral : 18.632 98.995 1542 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.81 % Allowed : 34.76 % Favored : 63.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.36), residues: 517 helix: 0.52 (0.24), residues: 414 sheet: None (None), residues: 0 loop : -2.57 (0.58), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.006 TRP A 95 HIS 0.004 0.001 HIS B 77 PHE 0.008 0.001 PHE B 38 TYR 0.013 0.002 TYR B 155 ARG 0.033 0.002 ARG B 56 Details of bonding type rmsd hydrogen bonds : bond 0.08409 ( 346) hydrogen bonds : angle 5.33111 ( 1038) covalent geometry : bond 0.00780 ( 4356) covalent geometry : angle 1.14055 ( 5874) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 162 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.8281 (mt) cc_final: 0.7699 (mm) REVERT: A 70 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7978 (mm-30) REVERT: A 273 TYR cc_start: 0.8557 (t80) cc_final: 0.8163 (t80) REVERT: B 21 LEU cc_start: 0.8227 (mt) cc_final: 0.7548 (mt) REVERT: B 48 GLN cc_start: 0.8144 (tm-30) cc_final: 0.7907 (tm-30) REVERT: B 70 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7968 (mm-30) REVERT: B 213 SER cc_start: 0.9059 (m) cc_final: 0.8751 (p) REVERT: B 289 TRP cc_start: 0.5463 (t60) cc_final: 0.4904 (t60) outliers start: 8 outliers final: 2 residues processed: 167 average time/residue: 0.1578 time to fit residues: 32.8627 Evaluate side-chains 154 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 152 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain B residue 80 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.130302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.107311 restraints weight = 8306.034| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 3.55 r_work: 0.3343 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 4356 Z= 0.243 Angle : 0.747 9.491 5874 Z= 0.379 Chirality : 0.040 0.192 645 Planarity : 0.005 0.042 728 Dihedral : 8.685 73.841 625 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.97 % Allowed : 29.12 % Favored : 65.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.38), residues: 517 helix: 1.67 (0.26), residues: 412 sheet: None (None), residues: 0 loop : -2.01 (0.61), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 95 HIS 0.004 0.001 HIS B 77 PHE 0.011 0.002 PHE B 225 TYR 0.031 0.002 TYR B 30 ARG 0.006 0.001 ARG A 56 Details of bonding type rmsd hydrogen bonds : bond 0.04286 ( 346) hydrogen bonds : angle 4.37114 ( 1038) covalent geometry : bond 0.00549 ( 4356) covalent geometry : angle 0.74686 ( 5874) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.431 Fit side-chains REVERT: A 51 GLN cc_start: 0.8859 (tt0) cc_final: 0.8382 (tp40) REVERT: A 70 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8038 (mm-30) REVERT: A 95 TRP cc_start: 0.5274 (t60) cc_final: 0.4538 (t60) REVERT: B 21 LEU cc_start: 0.7822 (mt) cc_final: 0.7541 (mt) REVERT: B 70 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8008 (mm-30) REVERT: B 95 TRP cc_start: 0.5158 (t60) cc_final: 0.4620 (t60) outliers start: 22 outliers final: 17 residues processed: 165 average time/residue: 0.1309 time to fit residues: 27.7653 Evaluate side-chains 152 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 279 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 30 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 15 optimal weight: 0.1980 chunk 12 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS A 254 GLN B 64 HIS B 254 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.133090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.110779 restraints weight = 8308.577| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.58 r_work: 0.3356 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4356 Z= 0.150 Angle : 0.667 9.750 5874 Z= 0.336 Chirality : 0.038 0.153 645 Planarity : 0.004 0.045 728 Dihedral : 6.432 41.802 619 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.71 % Allowed : 30.47 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.38), residues: 517 helix: 2.04 (0.26), residues: 414 sheet: None (None), residues: 0 loop : -1.39 (0.65), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 95 HIS 0.004 0.001 HIS A 77 PHE 0.008 0.001 PHE B 126 TYR 0.029 0.001 TYR B 30 ARG 0.010 0.001 ARG B 56 Details of bonding type rmsd hydrogen bonds : bond 0.03987 ( 346) hydrogen bonds : angle 4.20364 ( 1038) covalent geometry : bond 0.00323 ( 4356) covalent geometry : angle 0.66736 ( 5874) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.473 Fit side-chains REVERT: A 51 GLN cc_start: 0.8872 (tt0) cc_final: 0.8388 (tp40) REVERT: A 80 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8435 (tm-30) REVERT: A 95 TRP cc_start: 0.5274 (t60) cc_final: 0.4887 (t60) REVERT: A 220 GLU cc_start: 0.8293 (mp0) cc_final: 0.8090 (mp0) REVERT: B 51 GLN cc_start: 0.8783 (tt0) cc_final: 0.8392 (tp40) REVERT: B 80 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8509 (tm-30) REVERT: B 229 TYR cc_start: 0.9021 (t80) cc_final: 0.8496 (t80) outliers start: 12 outliers final: 12 residues processed: 157 average time/residue: 0.1202 time to fit residues: 25.0941 Evaluate side-chains 154 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 279 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 35 optimal weight: 0.7980 chunk 38 optimal weight: 0.3980 chunk 49 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 GLN ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.133530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.111336 restraints weight = 8223.018| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 3.51 r_work: 0.3349 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4356 Z= 0.139 Angle : 0.646 9.820 5874 Z= 0.324 Chirality : 0.038 0.160 645 Planarity : 0.004 0.048 728 Dihedral : 5.696 34.822 619 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 4.29 % Allowed : 30.70 % Favored : 65.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.39), residues: 517 helix: 2.20 (0.26), residues: 414 sheet: None (None), residues: 0 loop : -0.99 (0.69), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 95 HIS 0.007 0.001 HIS A 77 PHE 0.008 0.001 PHE A 225 TYR 0.030 0.001 TYR B 30 ARG 0.011 0.001 ARG B 56 Details of bonding type rmsd hydrogen bonds : bond 0.03796 ( 346) hydrogen bonds : angle 4.08660 ( 1038) covalent geometry : bond 0.00299 ( 4356) covalent geometry : angle 0.64606 ( 5874) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 48 GLN cc_start: 0.8468 (tm-30) cc_final: 0.8225 (tm-30) REVERT: A 51 GLN cc_start: 0.8847 (tt0) cc_final: 0.8347 (tp40) REVERT: A 77 HIS cc_start: 0.6693 (t-170) cc_final: 0.6432 (t-170) REVERT: A 158 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8959 (mmtt) REVERT: A 162 GLN cc_start: 0.9017 (tp-100) cc_final: 0.8776 (tp-100) REVERT: A 220 GLU cc_start: 0.8317 (mp0) cc_final: 0.8095 (mp0) REVERT: B 51 GLN cc_start: 0.8816 (tt0) cc_final: 0.8386 (tp40) REVERT: B 80 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8510 (tm-30) REVERT: B 158 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8932 (mmtt) REVERT: B 229 TYR cc_start: 0.9006 (t80) cc_final: 0.8382 (t80) outliers start: 19 outliers final: 11 residues processed: 158 average time/residue: 0.1165 time to fit residues: 24.2497 Evaluate side-chains 153 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 279 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 33 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 GLN ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.130264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.108358 restraints weight = 8331.466| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 3.46 r_work: 0.3334 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 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 : 0.003 0.026 4356 Z= 0.153 Angle : 0.695 16.227 5874 Z= 0.337 Chirality : 0.038 0.166 645 Planarity : 0.004 0.048 728 Dihedral : 5.410 32.571 619 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 4.97 % Allowed : 30.25 % Favored : 64.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.39), residues: 517 helix: 2.38 (0.26), residues: 414 sheet: None (None), residues: 0 loop : -0.73 (0.72), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 95 HIS 0.005 0.001 HIS B 77 PHE 0.010 0.001 PHE B 103 TYR 0.026 0.001 TYR B 30 ARG 0.010 0.001 ARG B 56 Details of bonding type rmsd hydrogen bonds : bond 0.03806 ( 346) hydrogen bonds : angle 4.00150 ( 1038) covalent geometry : bond 0.00333 ( 4356) covalent geometry : angle 0.69501 ( 5874) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLN cc_start: 0.8810 (tt0) cc_final: 0.8309 (tp40) REVERT: A 158 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8984 (mmtt) REVERT: B 51 GLN cc_start: 0.8786 (tt0) cc_final: 0.8374 (tp40) REVERT: B 80 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8518 (tm-30) REVERT: B 129 PHE cc_start: 0.8529 (m-80) cc_final: 0.8326 (m-80) REVERT: B 158 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8945 (mmtt) REVERT: B 162 GLN cc_start: 0.9061 (tp-100) cc_final: 0.8771 (tp-100) outliers start: 22 outliers final: 13 residues processed: 158 average time/residue: 0.1359 time to fit residues: 27.6150 Evaluate side-chains 156 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 279 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 2 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 GLN ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.129291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.107253 restraints weight = 8378.686| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 3.53 r_work: 0.3288 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4356 Z= 0.150 Angle : 0.720 16.263 5874 Z= 0.341 Chirality : 0.039 0.176 645 Planarity : 0.003 0.030 728 Dihedral : 5.289 31.022 619 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.39 % Allowed : 31.38 % Favored : 65.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.95 (0.39), residues: 517 helix: 2.50 (0.26), residues: 412 sheet: None (None), residues: 0 loop : -0.32 (0.75), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 95 HIS 0.006 0.001 HIS A 77 PHE 0.010 0.001 PHE A 103 TYR 0.027 0.001 TYR B 30 ARG 0.003 0.000 ARG B 56 Details of bonding type rmsd hydrogen bonds : bond 0.03781 ( 346) hydrogen bonds : angle 4.02059 ( 1038) covalent geometry : bond 0.00326 ( 4356) covalent geometry : angle 0.72030 ( 5874) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLN cc_start: 0.8796 (tt0) cc_final: 0.8312 (tp40) REVERT: A 158 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.9010 (mmtt) REVERT: B 51 GLN cc_start: 0.8784 (tt0) cc_final: 0.8390 (tp40) REVERT: B 129 PHE cc_start: 0.8499 (m-80) cc_final: 0.8120 (m-80) REVERT: B 158 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8960 (mmtt) REVERT: B 162 GLN cc_start: 0.9023 (tp-100) cc_final: 0.8696 (tp-100) outliers start: 15 outliers final: 12 residues processed: 153 average time/residue: 0.1434 time to fit residues: 28.5706 Evaluate side-chains 151 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 279 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 4 optimal weight: 5.9990 chunk 2 optimal weight: 0.1980 chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 GLN ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.129888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.107909 restraints weight = 8426.393| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 3.54 r_work: 0.3300 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4356 Z= 0.142 Angle : 0.727 16.546 5874 Z= 0.344 Chirality : 0.039 0.172 645 Planarity : 0.003 0.030 728 Dihedral : 5.196 29.893 619 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.84 % Allowed : 32.28 % Favored : 63.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (0.39), residues: 517 helix: 2.52 (0.26), residues: 412 sheet: None (None), residues: 0 loop : -0.37 (0.74), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 53 HIS 0.006 0.001 HIS B 77 PHE 0.010 0.001 PHE B 103 TYR 0.027 0.001 TYR B 30 ARG 0.002 0.000 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03737 ( 346) hydrogen bonds : angle 4.03413 ( 1038) covalent geometry : bond 0.00308 ( 4356) covalent geometry : angle 0.72692 ( 5874) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLN cc_start: 0.8803 (tt0) cc_final: 0.8308 (tp40) REVERT: A 158 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.9019 (mmtt) REVERT: A 162 GLN cc_start: 0.9006 (tp-100) cc_final: 0.8730 (tp-100) REVERT: A 215 MET cc_start: 0.9453 (ttp) cc_final: 0.8978 (ttp) REVERT: A 229 TYR cc_start: 0.9110 (t80) cc_final: 0.8277 (t80) REVERT: A 242 ASP cc_start: 0.8445 (p0) cc_final: 0.8073 (p0) REVERT: B 51 GLN cc_start: 0.8779 (tt0) cc_final: 0.8385 (tp40) REVERT: B 129 PHE cc_start: 0.8500 (m-80) cc_final: 0.8057 (m-80) REVERT: B 158 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8972 (mmtt) REVERT: B 229 TYR cc_start: 0.9065 (t80) cc_final: 0.8422 (t80) REVERT: B 242 ASP cc_start: 0.8571 (p0) cc_final: 0.8176 (p0) outliers start: 17 outliers final: 14 residues processed: 155 average time/residue: 0.1217 time to fit residues: 24.7639 Evaluate side-chains 158 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 95 TRP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 279 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 3 optimal weight: 1.9990 chunk 36 optimal weight: 0.0470 chunk 48 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 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 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 HIS A 254 GLN ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.130777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.108685 restraints weight = 8366.458| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 3.53 r_work: 0.3313 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4356 Z= 0.139 Angle : 0.744 17.510 5874 Z= 0.352 Chirality : 0.040 0.180 645 Planarity : 0.003 0.029 728 Dihedral : 5.098 28.748 619 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.84 % Allowed : 33.18 % Favored : 62.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (0.39), residues: 517 helix: 2.52 (0.26), residues: 412 sheet: None (None), residues: 0 loop : -0.39 (0.74), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP B 53 HIS 0.005 0.001 HIS A 77 PHE 0.009 0.001 PHE B 103 TYR 0.025 0.001 TYR B 30 ARG 0.003 0.000 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 346) hydrogen bonds : angle 4.07155 ( 1038) covalent geometry : bond 0.00299 ( 4356) covalent geometry : angle 0.74426 ( 5874) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLN cc_start: 0.8789 (tt0) cc_final: 0.8296 (tp40) REVERT: A 158 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.9029 (mmtt) REVERT: A 162 GLN cc_start: 0.9006 (tp-100) cc_final: 0.8699 (tp-100) REVERT: A 229 TYR cc_start: 0.9101 (t80) cc_final: 0.8258 (t80) REVERT: A 242 ASP cc_start: 0.8446 (p0) cc_final: 0.8096 (p0) REVERT: B 129 PHE cc_start: 0.8405 (m-80) cc_final: 0.8042 (m-80) REVERT: B 229 TYR cc_start: 0.9048 (t80) cc_final: 0.8424 (t80) REVERT: B 242 ASP cc_start: 0.8511 (p0) cc_final: 0.8127 (p0) outliers start: 17 outliers final: 11 residues processed: 155 average time/residue: 0.1270 time to fit residues: 25.8320 Evaluate side-chains 151 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 95 TRP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 279 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 23 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 GLN ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.129232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.106930 restraints weight = 8544.239| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 3.59 r_work: 0.3279 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4356 Z= 0.160 Angle : 0.781 17.212 5874 Z= 0.369 Chirality : 0.041 0.189 645 Planarity : 0.004 0.031 728 Dihedral : 5.123 28.805 619 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.93 % Allowed : 33.86 % Favored : 63.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (0.39), residues: 517 helix: 2.51 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -0.34 (0.75), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 53 HIS 0.006 0.001 HIS A 77 PHE 0.016 0.001 PHE A 129 TYR 0.026 0.001 TYR B 30 ARG 0.002 0.000 ARG A 72 Details of bonding type rmsd hydrogen bonds : bond 0.03789 ( 346) hydrogen bonds : angle 4.12717 ( 1038) covalent geometry : bond 0.00357 ( 4356) covalent geometry : angle 0.78102 ( 5874) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLN cc_start: 0.8817 (tt0) cc_final: 0.8324 (tp40) REVERT: A 162 GLN cc_start: 0.9028 (tp-100) cc_final: 0.8720 (tp-100) REVERT: B 51 GLN cc_start: 0.8812 (tt0) cc_final: 0.8409 (tp40) REVERT: B 129 PHE cc_start: 0.8438 (m-80) cc_final: 0.8017 (m-80) outliers start: 13 outliers final: 12 residues processed: 150 average time/residue: 0.1206 time to fit residues: 23.7713 Evaluate side-chains 154 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 95 TRP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 279 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 41 optimal weight: 0.0570 chunk 17 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 14 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 HIS A 254 GLN ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.129714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.107467 restraints weight = 8329.837| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 3.53 r_work: 0.3293 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4356 Z= 0.148 Angle : 0.779 17.450 5874 Z= 0.368 Chirality : 0.041 0.191 645 Planarity : 0.004 0.030 728 Dihedral : 5.087 28.226 619 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.48 % Allowed : 34.54 % Favored : 62.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.93 (0.39), residues: 517 helix: 2.49 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -0.34 (0.75), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 53 HIS 0.006 0.001 HIS A 77 PHE 0.008 0.001 PHE B 103 TYR 0.025 0.001 TYR B 30 ARG 0.002 0.000 ARG A 72 Details of bonding type rmsd hydrogen bonds : bond 0.03756 ( 346) hydrogen bonds : angle 4.14400 ( 1038) covalent geometry : bond 0.00326 ( 4356) covalent geometry : angle 0.77932 ( 5874) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLN cc_start: 0.8801 (tt0) cc_final: 0.8312 (tp40) REVERT: A 162 GLN cc_start: 0.8987 (tp-100) cc_final: 0.8680 (tp-100) REVERT: A 229 TYR cc_start: 0.9115 (t80) cc_final: 0.8340 (t80) REVERT: A 242 ASP cc_start: 0.8435 (p0) cc_final: 0.8073 (p0) REVERT: B 51 GLN cc_start: 0.8807 (tt0) cc_final: 0.8412 (tp40) REVERT: B 129 PHE cc_start: 0.8396 (m-80) cc_final: 0.7967 (m-80) REVERT: B 229 TYR cc_start: 0.9057 (t80) cc_final: 0.8456 (t80) REVERT: B 242 ASP cc_start: 0.8590 (p0) cc_final: 0.8202 (p0) outliers start: 11 outliers final: 11 residues processed: 146 average time/residue: 0.1202 time to fit residues: 23.2526 Evaluate side-chains 150 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 95 TRP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 279 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 29 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 14 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 26 optimal weight: 0.0980 chunk 46 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 HIS A 254 GLN ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.129129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.107131 restraints weight = 8413.778| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 3.55 r_work: 0.3287 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4356 Z= 0.151 Angle : 0.777 17.709 5874 Z= 0.366 Chirality : 0.041 0.186 645 Planarity : 0.004 0.028 728 Dihedral : 5.040 27.967 619 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.71 % Allowed : 34.76 % Favored : 62.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.39), residues: 517 helix: 2.53 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -0.31 (0.75), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 53 HIS 0.006 0.001 HIS B 77 PHE 0.020 0.001 PHE A 129 TYR 0.025 0.001 TYR B 30 ARG 0.002 0.000 ARG A 72 Details of bonding type rmsd hydrogen bonds : bond 0.03748 ( 346) hydrogen bonds : angle 4.16938 ( 1038) covalent geometry : bond 0.00332 ( 4356) covalent geometry : angle 0.77745 ( 5874) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2334.49 seconds wall clock time: 41 minutes 11.89 seconds (2471.89 seconds total)