Starting phenix.real_space_refine on Wed Jun 4 21:39:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jh1_61469/06_2025/9jh1_61469.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jh1_61469/06_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_61469/06_2025/9jh1_61469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jh1_61469/06_2025/9jh1_61469.map" model { file = "/net/cci-nas-00/data/ceres_data/9jh1_61469/06_2025/9jh1_61469.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jh1_61469/06_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-5710/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: 3.53, per 1000 atoms: 0.83 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: 1.30 Conformation dependent library (CDL) restraints added in 524.0 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: 0.38 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: 1.21 Time building geometry restraints manager: 1.50 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.720 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.190 ------------------------------------------------------------------------------- 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 : 0.484 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: 0.1591 time to fit residues: 33.1223 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 : 0.454 ------------------------------------------------------------------------------- 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 = 0.107310 restraints weight = 8306.035| |-----------------------------------------------------------------------------| 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 : 0.522 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: 0.4621 (t60) outliers start: 22 outliers final: 17 residues processed: 165 average time/residue: 0.1397 time to fit residues: 29.7657 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 : 0.479 ------------------------------------------------------------------------------- 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: 0.9990 chunk 41 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 15 optimal weight: 0.1980 chunk 12 optimal weight: 0.9980 chunk 48 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 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 = 0.3861 r_free = 0.3861 target = 0.133440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.111198 restraints weight = 8304.123| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 3.52 r_work: 0.3356 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2525 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= 0.152 Angle : 0.670 9.742 5874 Z= 0.337 Chirality : 0.038 0.153 645 Planarity : 0.004 0.045 728 Dihedral : 6.420 41.694 619 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 12.53 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: 2.09 (0.38), residues: 517 helix: 2.04 (0.26), residues: 414 sheet: None (None), residues: 0 loop : -1.39 (0.64), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 95 HIS 0.004 0.001 HIS B 77 PHE 0.007 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 0.03984 ( 346) hydrogen bonds : angle 4.20979 ( 1038) covalent geometry : bond 0.00329 ( 4356) covalent geometry : angle 0.66968 ( 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 158 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.490 Fit side-chains REVERT: A 51 GLN cc_start: 0.8879 (tt0) cc_final: 0.8393 (tp40) REVERT: A 80 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8433 (tm-30) REVERT: A 95 TRP cc_start: 0.5360 (t60) cc_final: 0.4804 (t60) REVERT: B 51 GLN cc_start: 0.8786 (tt0) cc_final: 0.8394 (tp40) REVERT: B 80 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8512 (tm-30) REVERT: B 220 GLU cc_start: 0.8359 (mp0) cc_final: 0.8155 (mp0) REVERT: B 229 TYR cc_start: 0.9023 (t80) cc_final: 0.8500 (t80) outliers start: 12 outliers final: 12 residues processed: 153 average time/residue: 0.1320 time to fit residues: 27.0840 Evaluate side-chains 155 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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: 2.9990 chunk 38 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3847 r_free = 0.3847 target = 0.131939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.109647 restraints weight = 8252.461| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 3.51 r_work: 0.3332 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4356 Z= 0.149 Angle : 0.653 9.825 5874 Z= 0.329 Chirality : 0.038 0.152 645 Planarity : 0.004 0.050 728 Dihedral : 5.741 34.716 619 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.74 % Allowed : 30.25 % 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: 2.43 (0.39), residues: 517 helix: 2.21 (0.26), residues: 414 sheet: None (None), residues: 0 loop : -0.96 (0.69), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 95 HIS 0.006 0.001 HIS A 77 PHE 0.009 0.001 PHE B 103 TYR 0.028 0.001 TYR B 30 ARG 0.010 0.001 ARG B 56 Details of bonding type rmsd hydrogen bonds : bond 0.03833 ( 346) hydrogen bonds : angle 4.10170 ( 1038) covalent geometry : bond 0.00327 ( 4356) covalent geometry : angle 0.65335 ( 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 165 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.493 Fit side-chains REVERT: A 51 GLN cc_start: 0.8783 (tt0) cc_final: 0.8307 (tp40) REVERT: A 158 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8967 (mmtt) REVERT: A 162 GLN cc_start: 0.9008 (tp-100) cc_final: 0.8763 (tp-100) REVERT: B 51 GLN cc_start: 0.8778 (tt0) cc_final: 0.8371 (tp40) REVERT: B 80 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8499 (tm-30) REVERT: B 158 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8963 (mmtt) REVERT: B 220 GLU cc_start: 0.8370 (mp0) cc_final: 0.8153 (mp0) REVERT: B 229 TYR cc_start: 0.9018 (t80) cc_final: 0.8395 (t80) outliers start: 21 outliers final: 12 residues processed: 159 average time/residue: 0.1218 time to fit residues: 25.5065 Evaluate side-chains 156 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 46 optimal weight: 0.0980 chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 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 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 = 0.3834 r_free = 0.3834 target = 0.130919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.108937 restraints weight = 8322.693| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 3.53 r_work: 0.3342 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3117 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= 0.140 Angle : 0.703 16.428 5874 Z= 0.336 Chirality : 0.038 0.167 645 Planarity : 0.004 0.051 728 Dihedral : 5.406 32.503 619 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % 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: 2.71 (0.39), residues: 517 helix: 2.36 (0.26), residues: 413 sheet: None (None), residues: 0 loop : -0.57 (0.73), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 95 HIS 0.006 0.001 HIS A 77 PHE 0.009 0.001 PHE B 38 TYR 0.026 0.001 TYR B 30 ARG 0.011 0.001 ARG B 56 Details of bonding type rmsd hydrogen bonds : bond 0.03774 ( 346) hydrogen bonds : angle 4.02173 ( 1038) covalent geometry : bond 0.00301 ( 4356) covalent geometry : angle 0.70289 ( 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 169 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLN cc_start: 0.8792 (tt0) cc_final: 0.8289 (tp40) REVERT: A 158 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8984 (mmtt) REVERT: A 215 MET cc_start: 0.9476 (ttp) cc_final: 0.9008 (ttp) REVERT: B 51 GLN cc_start: 0.8782 (tt0) cc_final: 0.8377 (tp40) REVERT: B 80 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8525 (tm-30) REVERT: B 158 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8951 (mmtt) REVERT: B 162 GLN cc_start: 0.9065 (tp-100) cc_final: 0.8775 (tp-100) REVERT: B 215 MET cc_start: 0.9456 (ttp) cc_final: 0.8974 (ttp) REVERT: B 229 TYR cc_start: 0.9042 (t80) cc_final: 0.8412 (t80) outliers start: 19 outliers final: 13 residues processed: 162 average time/residue: 0.1665 time to fit residues: 34.6780 Evaluate side-chains 158 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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 56 ARG Chi-restraints excluded: chain B residue 95 TRP 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: 0.9980 chunk 46 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.129263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.107233 restraints weight = 8380.814| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 3.54 r_work: 0.3293 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4356 Z= 0.153 Angle : 0.732 17.214 5874 Z= 0.345 Chirality : 0.039 0.168 645 Planarity : 0.004 0.044 728 Dihedral : 5.284 31.067 619 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.29 % Allowed : 31.38 % Favored : 64.33 % 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: 2.89 (0.39), residues: 517 helix: 2.46 (0.26), residues: 412 sheet: None (None), residues: 0 loop : -0.35 (0.75), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 53 HIS 0.003 0.001 HIS A 77 PHE 0.009 0.001 PHE A 103 TYR 0.027 0.001 TYR B 30 ARG 0.010 0.000 ARG B 56 Details of bonding type rmsd hydrogen bonds : bond 0.03801 ( 346) hydrogen bonds : angle 4.04438 ( 1038) covalent geometry : bond 0.00336 ( 4356) covalent geometry : angle 0.73174 ( 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 160 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLN cc_start: 0.8794 (tt0) cc_final: 0.8294 (tp40) REVERT: A 158 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.9000 (mmtt) REVERT: B 51 GLN cc_start: 0.8783 (tt0) cc_final: 0.8380 (tp40) REVERT: B 158 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8951 (mmtt) REVERT: B 215 MET cc_start: 0.9470 (ttp) cc_final: 0.8983 (ttp) outliers start: 19 outliers final: 14 residues processed: 154 average time/residue: 0.2060 time to fit residues: 40.6032 Evaluate side-chains 154 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 57 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 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: 0.6980 chunk 6 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 30 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3825 r_free = 0.3825 target = 0.129898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.107746 restraints weight = 8434.144| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 3.57 r_work: 0.3300 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4356 Z= 0.142 Angle : 0.718 15.731 5874 Z= 0.343 Chirality : 0.039 0.178 645 Planarity : 0.003 0.030 728 Dihedral : 5.221 29.998 619 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 11.71 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: 2.95 (0.39), residues: 517 helix: 2.51 (0.26), residues: 412 sheet: None (None), residues: 0 loop : -0.35 (0.75), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 53 HIS 0.006 0.001 HIS B 77 PHE 0.008 0.001 PHE A 225 TYR 0.026 0.001 TYR B 30 ARG 0.004 0.000 ARG B 56 Details of bonding type rmsd hydrogen bonds : bond 0.03774 ( 346) hydrogen bonds : angle 4.07371 ( 1038) covalent geometry : bond 0.00309 ( 4356) covalent geometry : angle 0.71785 ( 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 161 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLN cc_start: 0.8790 (tt0) cc_final: 0.8293 (tp40) REVERT: A 158 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.9030 (mmtt) REVERT: A 215 MET cc_start: 0.9515 (ttp) cc_final: 0.9033 (ttp) REVERT: A 229 TYR cc_start: 0.9117 (t80) cc_final: 0.8278 (t80) REVERT: A 242 ASP cc_start: 0.8446 (p0) cc_final: 0.8076 (p0) REVERT: B 51 GLN cc_start: 0.8774 (tt0) cc_final: 0.8390 (tp40) REVERT: B 158 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8999 (mmtt) REVERT: B 229 TYR cc_start: 0.9056 (t80) cc_final: 0.8426 (t80) REVERT: B 242 ASP cc_start: 0.8562 (p0) cc_final: 0.8168 (p0) outliers start: 17 outliers final: 14 residues processed: 154 average time/residue: 0.1572 time to fit residues: 32.1056 Evaluate side-chains 157 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 57 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 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: 0.0870 chunk 48 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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 = 0.3820 r_free = 0.3820 target = 0.129435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.107309 restraints weight = 8372.470| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 3.55 r_work: 0.3292 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3446 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= 0.150 Angle : 0.760 17.318 5874 Z= 0.358 Chirality : 0.040 0.184 645 Planarity : 0.003 0.030 728 Dihedral : 5.160 29.183 619 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.84 % Allowed : 32.05 % Favored : 64.11 % 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 (0.26), residues: 412 sheet: None (None), residues: 0 loop : -0.34 (0.75), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 95 HIS 0.005 0.001 HIS B 77 PHE 0.008 0.001 PHE A 225 TYR 0.025 0.001 TYR B 30 ARG 0.002 0.000 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03827 ( 346) hydrogen bonds : angle 4.12228 ( 1038) covalent geometry : bond 0.00329 ( 4356) covalent geometry : angle 0.76016 ( 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 161 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLN cc_start: 0.8801 (tt0) cc_final: 0.8315 (tp40) REVERT: A 215 MET cc_start: 0.9499 (ttp) cc_final: 0.9003 (ttp) REVERT: A 229 TYR cc_start: 0.9117 (t80) cc_final: 0.8230 (t80) REVERT: A 242 ASP cc_start: 0.8452 (p0) cc_final: 0.7884 (p0) REVERT: B 51 GLN cc_start: 0.8775 (tt0) cc_final: 0.8386 (tp40) REVERT: B 158 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.9001 (mmtt) REVERT: B 215 MET cc_start: 0.9517 (ttp) cc_final: 0.9037 (ttp) REVERT: B 229 TYR cc_start: 0.9065 (t80) cc_final: 0.8439 (t80) REVERT: B 242 ASP cc_start: 0.8544 (p0) cc_final: 0.8166 (p0) outliers start: 17 outliers final: 13 residues processed: 154 average time/residue: 0.1278 time to fit residues: 25.7700 Evaluate side-chains 157 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 57 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 158 LYS 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: 0.6980 chunk 49 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 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 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 = 0.129284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.107211 restraints weight = 8528.954| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 3.50 r_work: 0.3285 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3542 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= 0.157 Angle : 0.774 17.158 5874 Z= 0.367 Chirality : 0.041 0.191 645 Planarity : 0.003 0.030 728 Dihedral : 5.152 28.932 619 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.16 % Allowed : 33.63 % 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: 2.92 (0.39), residues: 517 helix: 2.47 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -0.28 (0.76), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 95 HIS 0.005 0.001 HIS B 77 PHE 0.008 0.001 PHE A 225 TYR 0.026 0.001 TYR B 30 ARG 0.002 0.000 ARG A 72 Details of bonding type rmsd hydrogen bonds : bond 0.03854 ( 346) hydrogen bonds : angle 4.18540 ( 1038) covalent geometry : bond 0.00346 ( 4356) covalent geometry : angle 0.77355 ( 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: 14 poor density : 142 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLN cc_start: 0.8829 (tt0) cc_final: 0.8335 (tp40) REVERT: A 215 MET cc_start: 0.9514 (ttp) cc_final: 0.9012 (ttp) REVERT: B 51 GLN cc_start: 0.8830 (tt0) cc_final: 0.8427 (tp40) outliers start: 14 outliers final: 13 residues processed: 150 average time/residue: 0.1584 time to fit residues: 32.0990 Evaluate side-chains 151 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 57 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: 1.9990 chunk 17 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 35 optimal weight: 0.4980 chunk 14 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 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 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 = 0.129601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.107402 restraints weight = 8355.843| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 3.55 r_work: 0.3297 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3613 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= 0.152 Angle : 0.783 17.525 5874 Z= 0.370 Chirality : 0.041 0.193 645 Planarity : 0.003 0.030 728 Dihedral : 5.117 28.531 619 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.93 % Allowed : 34.09 % 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: 2.95 (0.39), residues: 517 helix: 2.48 (0.26), residues: 412 sheet: None (None), residues: 0 loop : -0.22 (0.77), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 95 HIS 0.006 0.001 HIS B 77 PHE 0.022 0.001 PHE B 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 0.03855 ( 346) hydrogen bonds : angle 4.22085 ( 1038) covalent geometry : bond 0.00335 ( 4356) covalent geometry : angle 0.78282 ( 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 157 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLN cc_start: 0.8816 (tt0) cc_final: 0.8327 (tp40) REVERT: A 229 TYR cc_start: 0.9111 (t80) cc_final: 0.8327 (t80) REVERT: A 242 ASP cc_start: 0.8434 (p0) cc_final: 0.8096 (p0) REVERT: B 51 GLN cc_start: 0.8807 (tt0) cc_final: 0.8411 (tp40) REVERT: B 229 TYR cc_start: 0.9066 (t80) cc_final: 0.8452 (t80) REVERT: B 242 ASP cc_start: 0.8518 (p0) cc_final: 0.8118 (p0) outliers start: 13 outliers final: 13 residues processed: 151 average time/residue: 0.1175 time to fit residues: 23.5291 Evaluate side-chains 154 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 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 57 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 29 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 33 optimal weight: 0.3980 chunk 31 optimal weight: 0.2980 chunk 43 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 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 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 = 0.3826 r_free = 0.3826 target = 0.129639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.107760 restraints weight = 8438.683| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.50 r_work: 0.3295 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4356 Z= 0.150 Angle : 0.778 17.495 5874 Z= 0.369 Chirality : 0.040 0.189 645 Planarity : 0.003 0.027 728 Dihedral : 5.084 28.238 619 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.16 % Allowed : 34.31 % 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: 2.95 (0.39), residues: 517 helix: 2.48 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -0.23 (0.77), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP A 53 HIS 0.007 0.001 HIS A 77 PHE 0.021 0.001 PHE A 129 TYR 0.025 0.001 TYR B 30 ARG 0.002 0.000 ARG B 56 Details of bonding type rmsd hydrogen bonds : bond 0.03838 ( 346) hydrogen bonds : angle 4.23196 ( 1038) covalent geometry : bond 0.00327 ( 4356) covalent geometry : angle 0.77802 ( 5874) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2550.17 seconds wall clock time: 46 minutes 3.16 seconds (2763.16 seconds total)