Starting phenix.real_space_refine on Thu Jul 2 07:35:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pmp_17763/07_2026/8pmp_17763.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pmp_17763/07_2026/8pmp_17763.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8pmp_17763/07_2026/8pmp_17763.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pmp_17763/07_2026/8pmp_17763.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pmp_17763/07_2026/8pmp_17763.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pmp_17763/07_2026/8pmp_17763.map" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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 P 3 5.49 5 S 44 5.16 5 C 4820 2.51 5 N 1291 2.21 5 O 1396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7554 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6112 Classifications: {'peptide': 747} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 706} Chain breaks: 2 Chain: "B" Number of atoms: 1237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1237 Classifications: {'peptide': 152} Link IDs: {'TRANS': 151} Chain: "D" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 172 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 18} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'MGT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.82, per 1000 atoms: 0.24 Number of scatterers: 7554 At special positions: 0 Unit cell: (85.578, 94.807, 111.587, 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) S 44 16.00 P 3 15.00 O 1396 8.00 N 1291 7.00 C 4820 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 421.8 milliseconds 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1772 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 2 sheets defined 70.5% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 25 through 38 removed outlier: 3.849A pdb=" N VAL A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 60 Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 64 through 79 Processing helix chain 'A' and resid 82 through 97 Processing helix chain 'A' and resid 97 through 118 removed outlier: 3.706A pdb=" N GLY A 101 " --> pdb=" O ASN A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 137 removed outlier: 3.722A pdb=" N ALA A 124 " --> pdb=" O ASN A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 155 removed outlier: 3.657A pdb=" N MET A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 162 through 204 removed outlier: 3.829A pdb=" N ARG A 166 " --> pdb=" O PRO A 162 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 6.830A pdb=" N LYS A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLU A 183 " --> pdb=" O TRP A 179 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ALA A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLU A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 227 through 242 Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'A' and resid 256 through 262 Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 308 through 325 removed outlier: 3.671A pdb=" N PHE A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 346 through 361 Processing helix chain 'A' and resid 368 through 383 removed outlier: 3.587A pdb=" N TYR A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 401 Processing helix chain 'A' and resid 406 through 424 removed outlier: 3.651A pdb=" N PHE A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 433 Processing helix chain 'A' and resid 434 through 439 removed outlier: 3.903A pdb=" N SER A 438 " --> pdb=" O SER A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 459 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 470 through 477 removed outlier: 4.529A pdb=" N ALA A 475 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 513 through 523 removed outlier: 4.112A pdb=" N ASP A 523 " --> pdb=" O SER A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 555 Processing helix chain 'A' and resid 558 through 569 Processing helix chain 'A' and resid 569 through 577 removed outlier: 3.702A pdb=" N PHE A 573 " --> pdb=" O PHE A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 594 Processing helix chain 'A' and resid 597 through 611 Processing helix chain 'A' and resid 615 through 622 Processing helix chain 'A' and resid 628 through 632 Processing helix chain 'A' and resid 634 through 676 removed outlier: 3.967A pdb=" N TRP A 638 " --> pdb=" O ARG A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 732 Processing helix chain 'A' and resid 737 through 769 removed outlier: 5.737A pdb=" N GLN A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE A 757 " --> pdb=" O GLN A 753 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N GLN A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR A 761 " --> pdb=" O ILE A 757 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N VAL A 763 " --> pdb=" O GLN A 759 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N THR A 764 " --> pdb=" O GLN A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 789 removed outlier: 4.114A pdb=" N VAL A 781 " --> pdb=" O HIS A 777 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE A 782 " --> pdb=" O ILE A 778 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLN A 789 " --> pdb=" O PHE A 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 11 removed outlier: 3.620A pdb=" N ARG B 10 " --> pdb=" O LEU B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 39 removed outlier: 3.523A pdb=" N LYS B 38 " --> pdb=" O LYS B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 63 removed outlier: 4.021A pdb=" N ILE B 56 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 101 Processing helix chain 'B' and resid 133 through 139 Processing helix chain 'B' and resid 143 through 147 Processing helix chain 'B' and resid 150 through 155 Processing sheet with id=AA1, first strand: chain 'B' and resid 66 through 73 removed outlier: 5.132A pdb=" N PHE B 83 " --> pdb=" O GLY B 72 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR B 41 " --> pdb=" O ASP B 116 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 105 through 106 457 hydrogen bonds defined for protein. 1323 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: 1.16 Time building geometry restraints manager: 0.87 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: 2462 1.34 - 1.46: 1726 1.46 - 1.58: 3475 1.58 - 1.70: 5 1.70 - 1.82: 66 Bond restraints: 7734 Sorted by residual: bond pdb=" O3B MGT B 201 " pdb=" PG MGT B 201 " ideal model delta sigma weight residual 1.729 1.613 0.116 2.00e-02 2.50e+03 3.38e+01 bond pdb=" C5 MGT B 201 " pdb=" N7 MGT B 201 " ideal model delta sigma weight residual 1.423 1.324 0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" C4 MGT B 201 " pdb=" C5 MGT B 201 " ideal model delta sigma weight residual 1.377 1.476 -0.099 2.00e-02 2.50e+03 2.43e+01 bond pdb=" O3A MGT B 201 " pdb=" PB MGT B 201 " ideal model delta sigma weight residual 1.676 1.611 0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C1' MGT B 201 " pdb=" N9 MGT B 201 " ideal model delta sigma weight residual 1.428 1.493 -0.065 2.00e-02 2.50e+03 1.05e+01 ... (remaining 7729 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.80: 10433 3.80 - 7.60: 34 7.60 - 11.40: 4 11.40 - 15.20: 2 15.20 - 19.00: 1 Bond angle restraints: 10474 Sorted by residual: angle pdb=" C5 MGT B 201 " pdb=" N7 MGT B 201 " pdb=" CM7 MGT B 201 " ideal model delta sigma weight residual 111.85 130.85 -19.00 3.00e+00 1.11e-01 4.01e+01 angle pdb=" N3 MGT B 201 " pdb=" C4 MGT B 201 " pdb=" N9 MGT B 201 " ideal model delta sigma weight residual 124.54 138.79 -14.25 3.00e+00 1.11e-01 2.26e+01 angle pdb=" C5 MGT B 201 " pdb=" N7 MGT B 201 " pdb=" C8 MGT B 201 " ideal model delta sigma weight residual 102.03 115.17 -13.14 3.00e+00 1.11e-01 1.92e+01 angle pdb=" C4 MGT B 201 " pdb=" N9 MGT B 201 " pdb=" C8 MGT B 201 " ideal model delta sigma weight residual 105.60 116.82 -11.22 3.00e+00 1.11e-01 1.40e+01 angle pdb=" CA ILE D 856 " pdb=" C ILE D 856 " pdb=" O ILE D 856 " ideal model delta sigma weight residual 121.59 118.20 3.39 1.03e+00 9.43e-01 1.08e+01 ... (remaining 10469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 4159 17.49 - 34.98: 393 34.98 - 52.48: 84 52.48 - 69.97: 14 69.97 - 87.46: 12 Dihedral angle restraints: 4662 sinusoidal: 1940 harmonic: 2722 Sorted by residual: dihedral pdb=" CD ARG B 21 " pdb=" NE ARG B 21 " pdb=" CZ ARG B 21 " pdb=" NH1 ARG B 21 " ideal model delta sinusoidal sigma weight residual 0.00 35.28 -35.28 1 1.00e+01 1.00e-02 1.76e+01 dihedral pdb=" CA TYR D 859 " pdb=" C TYR D 859 " pdb=" N ARG D 860 " pdb=" CA ARG D 860 " ideal model delta harmonic sigma weight residual -180.00 -160.99 -19.01 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA ASN A 767 " pdb=" CB ASN A 767 " pdb=" CG ASN A 767 " pdb=" OD1 ASN A 767 " ideal model delta sinusoidal sigma weight residual -90.00 -161.10 71.10 2 2.00e+01 2.50e-03 1.07e+01 ... (remaining 4659 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 869 0.042 - 0.084: 210 0.084 - 0.126: 45 0.126 - 0.168: 9 0.168 - 0.210: 5 Chirality restraints: 1138 Sorted by residual: chirality pdb=" C2' MGT B 201 " pdb=" C1' MGT B 201 " pdb=" C3' MGT B 201 " pdb=" O2' MGT B 201 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CB ILE A 623 " pdb=" CA ILE A 623 " pdb=" CG1 ILE A 623 " pdb=" CG2 ILE A 623 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.83e-01 chirality pdb=" CA ILE D 856 " pdb=" N ILE D 856 " pdb=" C ILE D 856 " pdb=" CB ILE D 856 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.55e-01 ... (remaining 1135 not shown) Planarity restraints: 1343 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 21 " -0.506 9.50e-02 1.11e+02 2.28e-01 3.75e+01 pdb=" NE ARG B 21 " 0.045 2.00e-02 2.50e+03 pdb=" CZ ARG B 21 " -0.037 2.00e-02 2.50e+03 pdb=" NH1 ARG B 21 " 0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG B 21 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 621 " -0.025 2.00e-02 2.50e+03 5.14e-02 2.64e+01 pdb=" CG ASN A 621 " 0.089 2.00e-02 2.50e+03 pdb=" OD1 ASN A 621 " -0.033 2.00e-02 2.50e+03 pdb=" ND2 ASN A 621 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 269 " 0.065 5.00e-02 4.00e+02 9.76e-02 1.53e+01 pdb=" N PRO A 270 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO A 270 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 270 " 0.053 5.00e-02 4.00e+02 ... (remaining 1340 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 6 1.93 - 2.67: 180 2.67 - 3.42: 11501 3.42 - 4.16: 17505 4.16 - 4.90: 33011 Nonbonded interactions: 62203 Sorted by model distance: nonbonded pdb=" NE2 GLN A 599 " pdb=" O GLU B 54 " model vdw 1.191 3.120 nonbonded pdb=" NH2 ARG A 610 " pdb=" O LYS B 67 " model vdw 1.211 3.120 nonbonded pdb=" NE2 HIS A 597 " pdb=" OE1 GLU B 54 " model vdw 1.490 3.120 nonbonded pdb=" CE1 HIS A 597 " pdb=" OE1 GLU B 54 " model vdw 1.675 3.260 nonbonded pdb=" CZ ARG A 610 " pdb=" O LYS B 67 " model vdw 1.802 3.270 ... (remaining 62198 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.390 Find NCS groups from input model: 0.030 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: 0.010 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 7734 Z= 0.213 Angle : 0.741 19.004 10474 Z= 0.368 Chirality : 0.041 0.210 1138 Planarity : 0.008 0.228 1343 Dihedral : 14.541 87.459 2890 Min Nonbonded Distance : 1.191 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.86 % Favored : 96.81 % Rotamer: Outliers : 0.12 % Allowed : 10.72 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.30), residues: 910 helix: 1.55 (0.23), residues: 566 sheet: -2.19 (1.02), residues: 23 loop : 0.18 (0.38), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.042 0.001 ARG B 21 TYR 0.013 0.001 TYR A 169 PHE 0.028 0.002 PHE A 624 TRP 0.021 0.002 TRP A 416 HIS 0.003 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.21 ( 7734) covalent geometry : angle 0.74069 / 0.37 (10474) hydrogen bonds : bond 0.13194 / 8.83 ( 457) hydrogen bonds : angle 5.58443 / 3.97 ( 1323) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 265 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 ASP cc_start: 0.7212 (m-30) cc_final: 0.6925 (m-30) REVERT: A 189 ASP cc_start: 0.8222 (p0) cc_final: 0.7508 (p0) REVERT: A 337 VAL cc_start: 0.8358 (t) cc_final: 0.8019 (m) REVERT: A 371 MET cc_start: 0.8376 (tmm) cc_final: 0.7859 (tmm) REVERT: A 372 TYR cc_start: 0.5718 (m-80) cc_final: 0.5296 (m-80) REVERT: B 83 PHE cc_start: 0.7538 (p90) cc_final: 0.7129 (p90) REVERT: D 870 PHE cc_start: 0.8149 (m-80) cc_final: 0.7697 (m-10) outliers start: 1 outliers final: 1 residues processed: 266 average time/residue: 0.0969 time to fit residues: 33.3713 Evaluate side-chains 137 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 237 GLN A 383 GLN A 420 HIS A 649 ASN A 715 GLN A 724 HIS A 742 ASN A 748 GLN ** A 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 55 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.115073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.096358 restraints weight = 24595.273| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 5.26 r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7734 Z= 0.174 Angle : 0.756 13.308 10474 Z= 0.372 Chirality : 0.046 0.256 1138 Planarity : 0.006 0.094 1343 Dihedral : 5.337 79.395 1008 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.49 % Allowed : 16.02 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.29), residues: 910 helix: 1.67 (0.22), residues: 584 sheet: -1.85 (0.96), residues: 22 loop : 0.26 (0.39), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 610 TYR 0.015 0.002 TYR A 169 PHE 0.016 0.002 PHE B 83 TRP 0.018 0.001 TRP A 416 HIS 0.006 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 ( 7734) covalent geometry : angle 0.75618 / 0.37 (10474) hydrogen bonds : bond 0.04554 / 3.04 ( 457) hydrogen bonds : angle 4.44005 / 3.22 ( 1323) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ARG cc_start: 0.7390 (mmm160) cc_final: 0.7183 (ptt90) REVERT: A 189 ASP cc_start: 0.8204 (p0) cc_final: 0.7666 (p0) REVERT: A 371 MET cc_start: 0.8450 (tmm) cc_final: 0.7777 (tmm) REVERT: A 607 LYS cc_start: 0.8253 (tptm) cc_final: 0.7832 (tppt) REVERT: B 24 HIS cc_start: 0.7919 (m90) cc_final: 0.7697 (m90) REVERT: B 83 PHE cc_start: 0.7275 (p90) cc_final: 0.6365 (p90) REVERT: B 95 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8053 (mp0) REVERT: B 98 MET cc_start: 0.8568 (mmm) cc_final: 0.8267 (mmm) outliers start: 29 outliers final: 12 residues processed: 169 average time/residue: 0.0832 time to fit residues: 19.0735 Evaluate side-chains 128 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 483 CYS Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 95 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 70 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 597 HIS A 715 GLN ** A 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.112012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.093252 restraints weight = 24688.557| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 5.15 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 7734 Z= 0.162 Angle : 0.686 13.255 10474 Z= 0.338 Chirality : 0.044 0.185 1138 Planarity : 0.005 0.043 1343 Dihedral : 5.127 75.181 1008 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.61 % Allowed : 16.99 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.28), residues: 910 helix: 1.61 (0.21), residues: 584 sheet: -1.95 (0.94), residues: 22 loop : 0.14 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 129 TYR 0.018 0.002 TYR D 859 PHE 0.015 0.002 PHE A 632 TRP 0.017 0.001 TRP A 416 HIS 0.005 0.001 HIS A 724 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 ( 7734) covalent geometry : angle 0.68598 / 0.34 (10474) hydrogen bonds : bond 0.04260 / 2.84 ( 457) hydrogen bonds : angle 4.38878 / 3.19 ( 1323) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 ASP cc_start: 0.8220 (p0) cc_final: 0.7633 (p0) REVERT: A 324 SER cc_start: 0.9183 (m) cc_final: 0.8910 (p) REVERT: A 371 MET cc_start: 0.8364 (tmm) cc_final: 0.7755 (tmm) REVERT: A 401 ARG cc_start: 0.7577 (mtt-85) cc_final: 0.7345 (mtt90) REVERT: A 607 LYS cc_start: 0.8258 (tptm) cc_final: 0.7756 (tppt) REVERT: A 715 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7566 (pp30) REVERT: A 719 MET cc_start: 0.8438 (ppp) cc_final: 0.7901 (ptm) REVERT: B 30 GLU cc_start: 0.9368 (mm-30) cc_final: 0.9145 (mm-30) REVERT: B 55 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7943 (pt0) REVERT: B 98 MET cc_start: 0.8726 (mmm) cc_final: 0.8504 (mmm) outliers start: 30 outliers final: 15 residues processed: 148 average time/residue: 0.0756 time to fit residues: 15.3849 Evaluate side-chains 124 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 483 CYS Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 715 GLN Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 114 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 83 optimal weight: 0.3980 chunk 58 optimal weight: 0.0270 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 overall best weight: 1.2842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 HIS ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 649 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.107904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.089102 restraints weight = 25123.608| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 5.20 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 7734 Z= 0.188 Angle : 0.701 13.186 10474 Z= 0.346 Chirality : 0.044 0.157 1138 Planarity : 0.005 0.040 1343 Dihedral : 4.894 66.395 1008 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.98 % Allowed : 17.47 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.28), residues: 910 helix: 1.61 (0.21), residues: 581 sheet: -2.23 (0.88), residues: 22 loop : 0.12 (0.37), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 21 TYR 0.018 0.002 TYR A 169 PHE 0.015 0.002 PHE A 624 TRP 0.017 0.001 TRP A 416 HIS 0.004 0.001 HIS A 724 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 ( 7734) covalent geometry : angle 0.70054 / 0.35 (10474) hydrogen bonds : bond 0.04252 / 2.84 ( 457) hydrogen bonds : angle 4.36519 / 3.19 ( 1323) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 ASP cc_start: 0.8297 (p0) cc_final: 0.7743 (p0) REVERT: A 291 MET cc_start: 0.8806 (ppp) cc_final: 0.8088 (ppp) REVERT: A 324 SER cc_start: 0.9211 (m) cc_final: 0.8948 (p) REVERT: A 371 MET cc_start: 0.8438 (tmm) cc_final: 0.7713 (tmm) REVERT: A 372 TYR cc_start: 0.7039 (m-80) cc_final: 0.6772 (m-10) REVERT: A 504 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8952 (mm) REVERT: A 597 HIS cc_start: 0.7310 (OUTLIER) cc_final: 0.6201 (t-90) REVERT: A 600 MET cc_start: 0.7805 (tpt) cc_final: 0.7281 (tpt) REVERT: B 55 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7819 (pt0) REVERT: B 95 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8101 (mp0) outliers start: 33 outliers final: 19 residues processed: 141 average time/residue: 0.0698 time to fit residues: 13.6535 Evaluate side-chains 129 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 597 HIS Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 137 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 17 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 GLN A 649 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.109156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.090725 restraints weight = 24580.045| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 5.12 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.5122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 7734 Z= 0.153 Angle : 0.683 13.289 10474 Z= 0.335 Chirality : 0.043 0.205 1138 Planarity : 0.004 0.048 1343 Dihedral : 4.779 63.216 1007 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.77 % Allowed : 19.40 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.28), residues: 910 helix: 1.62 (0.21), residues: 587 sheet: -1.84 (1.08), residues: 16 loop : 0.16 (0.37), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 401 TYR 0.020 0.002 TYR D 859 PHE 0.017 0.002 PHE A 624 TRP 0.017 0.001 TRP A 416 HIS 0.012 0.001 HIS A 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 ( 7734) covalent geometry : angle 0.68326 / 0.34 (10474) hydrogen bonds : bond 0.04079 / 2.75 ( 457) hydrogen bonds : angle 4.28460 / 3.16 ( 1323) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 CYS cc_start: 0.8530 (t) cc_final: 0.8256 (p) REVERT: A 189 ASP cc_start: 0.8309 (p0) cc_final: 0.7769 (p0) REVERT: A 291 MET cc_start: 0.8764 (ppp) cc_final: 0.7967 (ppp) REVERT: A 324 SER cc_start: 0.9227 (m) cc_final: 0.8994 (p) REVERT: A 371 MET cc_start: 0.8446 (tmm) cc_final: 0.7698 (tmm) REVERT: A 504 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8936 (mm) outliers start: 23 outliers final: 17 residues processed: 130 average time/residue: 0.0687 time to fit residues: 12.6155 Evaluate side-chains 123 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 725 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 ASN A 319 HIS A 419 HIS A 439 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.107953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.089413 restraints weight = 25096.206| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 5.15 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.5450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 7734 Z= 0.146 Angle : 0.669 13.235 10474 Z= 0.328 Chirality : 0.043 0.246 1138 Planarity : 0.004 0.042 1343 Dihedral : 4.734 58.507 1007 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.49 % Allowed : 19.40 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.28), residues: 910 helix: 1.76 (0.21), residues: 587 sheet: -1.70 (1.08), residues: 16 loop : 0.08 (0.37), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 746 TYR 0.016 0.002 TYR D 859 PHE 0.021 0.002 PHE A 624 TRP 0.015 0.001 TRP A 416 HIS 0.005 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 7734) covalent geometry : angle 0.66906 / 0.33 (10474) hydrogen bonds : bond 0.03963 / 2.65 ( 457) hydrogen bonds : angle 4.25516 / 3.16 ( 1323) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ARG cc_start: 0.7630 (mmm160) cc_final: 0.7242 (ptt90) REVERT: A 189 ASP cc_start: 0.8342 (p0) cc_final: 0.7783 (p0) REVERT: A 291 MET cc_start: 0.8780 (ppp) cc_final: 0.7944 (ppp) REVERT: A 317 ASN cc_start: 0.8670 (m-40) cc_final: 0.8162 (m110) REVERT: A 371 MET cc_start: 0.8385 (tmm) cc_final: 0.7661 (tmm) REVERT: A 372 TYR cc_start: 0.7299 (m-10) cc_final: 0.6888 (m-10) REVERT: A 401 ARG cc_start: 0.7845 (mtt-85) cc_final: 0.7521 (mtt90) REVERT: B 95 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.8064 (mp0) outliers start: 29 outliers final: 19 residues processed: 130 average time/residue: 0.0719 time to fit residues: 13.1249 Evaluate side-chains 121 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 95 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 84 optimal weight: 0.0970 chunk 23 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 45 optimal weight: 0.0980 chunk 6 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 89 optimal weight: 0.3980 chunk 80 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN A 245 GLN B 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.109506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.090065 restraints weight = 24315.567| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 5.22 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.5688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 7734 Z= 0.129 Angle : 0.651 13.245 10474 Z= 0.317 Chirality : 0.041 0.189 1138 Planarity : 0.004 0.042 1343 Dihedral : 4.701 56.821 1007 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.49 % Allowed : 19.64 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.28), residues: 910 helix: 1.80 (0.21), residues: 587 sheet: -1.61 (1.01), residues: 21 loop : 0.09 (0.38), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 77 TYR 0.015 0.002 TYR D 859 PHE 0.028 0.002 PHE A 624 TRP 0.013 0.001 TRP A 416 HIS 0.004 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 7734) covalent geometry : angle 0.65105 / 0.32 (10474) hydrogen bonds : bond 0.03766 / 2.54 ( 457) hydrogen bonds : angle 4.14789 / 3.08 ( 1323) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 ASP cc_start: 0.8321 (p0) cc_final: 0.7744 (p0) REVERT: A 291 MET cc_start: 0.8823 (ppp) cc_final: 0.7930 (ppp) REVERT: A 371 MET cc_start: 0.8366 (tmm) cc_final: 0.7706 (tmm) REVERT: A 401 ARG cc_start: 0.7944 (mtt-85) cc_final: 0.7646 (mtt90) REVERT: A 504 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8803 (mm) REVERT: B 95 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8052 (mp0) outliers start: 29 outliers final: 18 residues processed: 129 average time/residue: 0.0732 time to fit residues: 13.2581 Evaluate side-chains 121 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 95 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 74 optimal weight: 0.0270 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 50 optimal weight: 0.0060 chunk 3 optimal weight: 0.7980 overall best weight: 0.4454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 367 HIS A 649 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.108766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.090636 restraints weight = 24666.675| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 5.13 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.5841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 7734 Z= 0.133 Angle : 0.677 13.210 10474 Z= 0.326 Chirality : 0.042 0.250 1138 Planarity : 0.004 0.042 1343 Dihedral : 4.682 57.171 1007 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.65 % Allowed : 20.96 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.28), residues: 910 helix: 1.75 (0.21), residues: 587 sheet: -1.59 (1.01), residues: 21 loop : 0.11 (0.38), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 77 TYR 0.041 0.002 TYR B 100 PHE 0.016 0.001 PHE A 573 TRP 0.013 0.001 TRP A 416 HIS 0.005 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 7734) covalent geometry : angle 0.67678 / 0.33 (10474) hydrogen bonds : bond 0.03770 / 2.57 ( 457) hydrogen bonds : angle 4.22541 / 3.14 ( 1323) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 ASP cc_start: 0.8349 (p0) cc_final: 0.7807 (p0) REVERT: A 291 MET cc_start: 0.8836 (ppp) cc_final: 0.8024 (ppp) REVERT: A 335 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7770 (mt0) REVERT: A 371 MET cc_start: 0.8336 (tmm) cc_final: 0.7712 (tmm) REVERT: A 592 GLU cc_start: 0.8208 (tt0) cc_final: 0.7950 (pt0) REVERT: B 95 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8057 (mp0) REVERT: B 102 ASN cc_start: 0.8534 (t0) cc_final: 0.8263 (t0) outliers start: 22 outliers final: 19 residues processed: 128 average time/residue: 0.0676 time to fit residues: 12.1137 Evaluate side-chains 124 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 95 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 58 optimal weight: 0.1980 chunk 20 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 24 optimal weight: 0.0670 chunk 27 optimal weight: 0.3980 chunk 8 optimal weight: 0.7980 chunk 63 optimal weight: 8.9990 chunk 33 optimal weight: 0.0770 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 462 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.109449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.091324 restraints weight = 24330.139| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 5.10 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.5995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 7734 Z= 0.133 Angle : 0.679 13.213 10474 Z= 0.328 Chirality : 0.042 0.223 1138 Planarity : 0.004 0.050 1343 Dihedral : 4.690 57.039 1007 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.65 % Allowed : 22.05 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.28), residues: 910 helix: 1.82 (0.21), residues: 581 sheet: -1.56 (1.01), residues: 21 loop : 0.06 (0.38), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 401 TYR 0.033 0.002 TYR B 100 PHE 0.024 0.001 PHE A 104 TRP 0.017 0.001 TRP A 430 HIS 0.008 0.001 HIS A 754 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 7734) covalent geometry : angle 0.67904 / 0.33 (10474) hydrogen bonds : bond 0.03773 / 2.55 ( 457) hydrogen bonds : angle 4.25775 / 3.16 ( 1323) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 ASP cc_start: 0.8283 (p0) cc_final: 0.8065 (p0) REVERT: A 291 MET cc_start: 0.8844 (ppp) cc_final: 0.8060 (ppp) REVERT: A 371 MET cc_start: 0.8319 (tmm) cc_final: 0.7679 (tmm) REVERT: A 592 GLU cc_start: 0.8241 (tt0) cc_final: 0.8038 (tt0) REVERT: B 69 ILE cc_start: 0.8447 (mm) cc_final: 0.8242 (tp) REVERT: B 95 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8037 (mp0) REVERT: B 102 ASN cc_start: 0.8493 (t0) cc_final: 0.8263 (t0) REVERT: D 858 GLU cc_start: 0.7721 (tp30) cc_final: 0.7289 (pm20) outliers start: 22 outliers final: 17 residues processed: 121 average time/residue: 0.0674 time to fit residues: 11.5043 Evaluate side-chains 118 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 95 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 67 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 11 optimal weight: 0.0970 chunk 16 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 20 optimal weight: 0.0030 chunk 82 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 649 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.109171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.091053 restraints weight = 24263.294| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 5.05 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.6152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 7734 Z= 0.137 Angle : 0.704 13.192 10474 Z= 0.341 Chirality : 0.042 0.210 1138 Planarity : 0.005 0.050 1343 Dihedral : 4.724 57.948 1007 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.29 % Allowed : 22.65 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.28), residues: 910 helix: 1.67 (0.21), residues: 587 sheet: -1.41 (0.97), residues: 23 loop : -0.12 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 401 TYR 0.031 0.002 TYR B 100 PHE 0.018 0.001 PHE A 149 TRP 0.018 0.001 TRP A 430 HIS 0.009 0.001 HIS A 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 7734) covalent geometry : angle 0.70433 / 0.34 (10474) hydrogen bonds : bond 0.03842 / 2.60 ( 457) hydrogen bonds : angle 4.28818 / 3.20 ( 1323) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 ASP cc_start: 0.8532 (p0) cc_final: 0.8098 (p0) REVERT: A 291 MET cc_start: 0.8710 (ppp) cc_final: 0.8325 (ppp) REVERT: A 371 MET cc_start: 0.8348 (tmm) cc_final: 0.7706 (tmm) REVERT: A 457 MET cc_start: 0.7395 (ttm) cc_final: 0.7180 (tpt) REVERT: A 592 GLU cc_start: 0.8206 (tt0) cc_final: 0.7992 (pt0) REVERT: B 95 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.8033 (mp0) REVERT: B 102 ASN cc_start: 0.8479 (t0) cc_final: 0.8264 (t0) REVERT: D 858 GLU cc_start: 0.7641 (tp30) cc_final: 0.7249 (pm20) outliers start: 19 outliers final: 15 residues processed: 111 average time/residue: 0.0612 time to fit residues: 9.8362 Evaluate side-chains 112 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 95 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 17 optimal weight: 0.5980 chunk 85 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 70 optimal weight: 0.2980 chunk 86 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.107476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.089561 restraints weight = 24376.844| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 5.19 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.6332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 7734 Z= 0.144 Angle : 0.693 13.180 10474 Z= 0.337 Chirality : 0.042 0.199 1138 Planarity : 0.005 0.087 1343 Dihedral : 4.726 59.712 1007 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.05 % Allowed : 22.77 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.28), residues: 910 helix: 1.66 (0.21), residues: 592 sheet: -1.59 (0.96), residues: 21 loop : -0.18 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 401 TYR 0.029 0.002 TYR B 100 PHE 0.027 0.001 PHE A 104 TRP 0.017 0.001 TRP A 430 HIS 0.007 0.001 HIS A 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.14 ( 7734) covalent geometry : angle 0.69326 / 0.34 (10474) hydrogen bonds : bond 0.03849 / 2.58 ( 457) hydrogen bonds : angle 4.26748 / 3.17 ( 1323) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1444.51 seconds wall clock time: 25 minutes 38.59 seconds (1538.59 seconds total)