Starting phenix.real_space_refine on Fri Aug 22 14:59:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8teg_41185/08_2025/8teg_41185.cif Found real_map, /net/cci-nas-00/data/ceres_data/8teg_41185/08_2025/8teg_41185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8teg_41185/08_2025/8teg_41185.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8teg_41185/08_2025/8teg_41185.map" model { file = "/net/cci-nas-00/data/ceres_data/8teg_41185/08_2025/8teg_41185.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8teg_41185/08_2025/8teg_41185.cif" } resolution = 2.15 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 2926 2.51 5 N 716 2.21 5 O 846 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4518 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4247 Classifications: {'peptide': 539} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 503} Chain breaks: 2 Chain: "B" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 183 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 1, 'TRANS': 20} Chain: "A" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Time building chain proxies: 1.30, per 1000 atoms: 0.29 Number of scatterers: 4518 At special positions: 0 Unit cell: (73.87, 90.47, 84.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 846 8.00 N 716 7.00 C 2926 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: 0.27 Conformation dependent library (CDL) restraints added in 139.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1036 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 3 sheets defined 76.6% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 8 through 20 removed outlier: 3.772A pdb=" N MET A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 31 removed outlier: 4.057A pdb=" N GLY A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 35 removed outlier: 3.776A pdb=" N ARG A 35 " --> pdb=" O ALA A 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 32 through 35' Processing helix chain 'A' and resid 36 through 62 removed outlier: 3.610A pdb=" N ILE A 49 " --> pdb=" O PHE A 45 " (cutoff:3.500A) Proline residue: A 50 - end of helix Processing helix chain 'A' and resid 67 through 86 Processing helix chain 'A' and resid 96 through 112 removed outlier: 3.539A pdb=" N ALA A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 142 Processing helix chain 'A' and resid 143 through 151 removed outlier: 3.521A pdb=" N ILE A 147 " --> pdb=" O ALA A 144 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE A 148 " --> pdb=" O CYS A 145 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ASN A 149 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 178 removed outlier: 3.517A pdb=" N LEU A 158 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 192 Processing helix chain 'A' and resid 193 through 219 removed outlier: 3.542A pdb=" N ARG A 219 " --> pdb=" O GLY A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 228 through 252 removed outlier: 6.235A pdb=" N VAL A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Proline residue: A 241 - end of helix Processing helix chain 'A' and resid 253 through 258 removed outlier: 4.572A pdb=" N GLY A 256 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL A 258 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 290 through 297 Processing helix chain 'A' and resid 297 through 320 removed outlier: 3.615A pdb=" N MET A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER A 313 " --> pdb=" O TYR A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 325 Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'A' and resid 359 through 368 Processing helix chain 'A' and resid 464 through 480 removed outlier: 3.924A pdb=" N VAL A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA A 479 " --> pdb=" O GLY A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 Processing helix chain 'A' and resid 488 through 503 removed outlier: 3.696A pdb=" N LEU A 492 " --> pdb=" O PRO A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 517 Processing helix chain 'A' and resid 519 through 521 No H-bonds generated for 'chain 'A' and resid 519 through 521' Processing helix chain 'A' and resid 522 through 528 removed outlier: 3.923A pdb=" N VAL A 526 " --> pdb=" O ARG A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 538 Processing helix chain 'A' and resid 539 through 561 Processing helix chain 'A' and resid 565 through 568 Processing helix chain 'A' and resid 569 through 584 removed outlier: 3.526A pdb=" N MET A 573 " --> pdb=" O MET A 569 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU A 577 " --> pdb=" O MET A 573 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE A 578 " --> pdb=" O ILE A 574 " (cutoff:3.500A) Proline residue: A 579 - end of helix Processing helix chain 'A' and resid 584 through 589 removed outlier: 3.709A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 598 Processing helix chain 'A' and resid 609 through 614 Processing helix chain 'B' and resid 626 through 635 removed outlier: 3.731A pdb=" N GLU B 633 " --> pdb=" O GLU B 629 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 94 Processing sheet with id=AA2, first strand: chain 'A' and resid 369 through 371 Processing sheet with id=AA3, first strand: chain 'A' and resid 531 through 532 277 hydrogen bonds defined for protein. 795 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.47 Time building geometry restraints manager: 0.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.24: 568 1.24 - 1.38: 1174 1.38 - 1.53: 2133 1.53 - 1.67: 626 1.67 - 1.81: 52 Bond restraints: 4553 Sorted by residual: bond pdb=" CG PRO A 114 " pdb=" CD PRO A 114 " ideal model delta sigma weight residual 1.503 1.099 0.404 3.40e-02 8.65e+02 1.41e+02 bond pdb=" N PRO A 114 " pdb=" CA PRO A 114 " ideal model delta sigma weight residual 1.471 1.521 -0.050 1.32e-02 5.74e+03 1.42e+01 bond pdb=" N PRO A 114 " pdb=" CD PRO A 114 " ideal model delta sigma weight residual 1.473 1.515 -0.042 1.40e-02 5.10e+03 8.90e+00 bond pdb=" CA PRO A 114 " pdb=" CB PRO A 114 " ideal model delta sigma weight residual 1.534 1.509 0.025 1.43e-02 4.89e+03 3.05e+00 bond pdb=" N PHE A 5 " pdb=" CA PHE A 5 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 ... (remaining 4548 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.01: 6179 5.01 - 10.02: 5 10.02 - 15.02: 0 15.02 - 20.03: 0 20.03 - 25.04: 2 Bond angle restraints: 6186 Sorted by residual: angle pdb=" N PRO A 114 " pdb=" CD PRO A 114 " pdb=" CG PRO A 114 " ideal model delta sigma weight residual 103.20 78.16 25.04 1.50e+00 4.44e-01 2.79e+02 angle pdb=" CA PRO A 114 " pdb=" CB PRO A 114 " pdb=" CG PRO A 114 " ideal model delta sigma weight residual 104.50 79.68 24.82 1.90e+00 2.77e-01 1.71e+02 angle pdb=" N PRO A 114 " pdb=" CA PRO A 114 " pdb=" CB PRO A 114 " ideal model delta sigma weight residual 103.30 97.17 6.13 1.12e+00 7.97e-01 3.00e+01 angle pdb=" CA PRO A 114 " pdb=" N PRO A 114 " pdb=" CD PRO A 114 " ideal model delta sigma weight residual 112.00 105.20 6.80 1.40e+00 5.10e-01 2.36e+01 angle pdb=" N LEU A 504 " pdb=" CA LEU A 504 " pdb=" C LEU A 504 " ideal model delta sigma weight residual 109.81 116.27 -6.46 2.21e+00 2.05e-01 8.54e+00 ... (remaining 6181 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 2360 17.69 - 35.39: 245 35.39 - 53.08: 52 53.08 - 70.78: 9 70.78 - 88.47: 8 Dihedral angle restraints: 2674 sinusoidal: 1062 harmonic: 1612 Sorted by residual: dihedral pdb=" CA LYS A 590 " pdb=" C LYS A 590 " pdb=" N GLY A 591 " pdb=" CA GLY A 591 " ideal model delta harmonic sigma weight residual 180.00 157.04 22.96 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" N PRO A 114 " pdb=" CG PRO A 114 " pdb=" CD PRO A 114 " pdb=" CB PRO A 114 " ideal model delta sinusoidal sigma weight residual 30.00 81.50 -51.50 1 1.50e+01 4.44e-03 1.61e+01 dihedral pdb=" CA LEU A 504 " pdb=" C LEU A 504 " pdb=" N PRO A 505 " pdb=" CA PRO A 505 " ideal model delta harmonic sigma weight residual -180.00 -160.62 -19.38 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 2671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 444 0.030 - 0.060: 173 0.060 - 0.090: 51 0.090 - 0.120: 23 0.120 - 0.150: 7 Chirality restraints: 698 Sorted by residual: chirality pdb=" CA ILE A 358 " pdb=" N ILE A 358 " pdb=" C ILE A 358 " pdb=" CB ILE A 358 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.64e-01 chirality pdb=" CA PRO A 505 " pdb=" N PRO A 505 " pdb=" C PRO A 505 " pdb=" CB PRO A 505 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CA PRO A 564 " pdb=" N PRO A 564 " pdb=" C PRO A 564 " pdb=" CB PRO A 564 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 695 not shown) Planarity restraints: 769 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 580 " 0.006 2.00e-02 2.50e+03 1.17e-02 1.37e+00 pdb=" C VAL A 580 " -0.020 2.00e-02 2.50e+03 pdb=" O VAL A 580 " 0.008 2.00e-02 2.50e+03 pdb=" N ARG A 581 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 97 " -0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO A 98 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 98 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 98 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 253 " -0.016 5.00e-02 4.00e+02 2.47e-02 9.76e-01 pdb=" N PRO A 254 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO A 254 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 254 " -0.014 5.00e-02 4.00e+02 ... (remaining 766 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 226 2.73 - 3.27: 4804 3.27 - 3.81: 7945 3.81 - 4.36: 9877 4.36 - 4.90: 15723 Nonbonded interactions: 38575 Sorted by model distance: nonbonded pdb=" O ALA A 144 " pdb=" OH TYR A 309 " model vdw 2.185 3.040 nonbonded pdb=" OD1 ASP A 25 " pdb=" NZ LYS A 328 " model vdw 2.317 3.120 nonbonded pdb=" N GLU A 323 " pdb=" OE1 GLU A 323 " model vdw 2.414 3.120 nonbonded pdb=" OD2 ASP A 335 " pdb=" O HOH A 801 " model vdw 2.419 3.040 nonbonded pdb=" O LYS A 260 " pdb=" O HOH A 802 " model vdw 2.442 3.040 ... (remaining 38570 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: 3.960 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.660 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 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 : 0.007 0.404 4553 Z= 0.238 Angle : 0.742 25.041 6186 Z= 0.415 Chirality : 0.039 0.150 698 Planarity : 0.004 0.027 769 Dihedral : 15.683 88.472 1638 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.05 % Allowed : 9.28 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.36), residues: 553 helix: 1.36 (0.27), residues: 384 sheet: -1.48 (1.36), residues: 10 loop : 1.33 (0.50), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 222 TYR 0.013 0.001 TYR A 495 PHE 0.012 0.001 PHE A 534 TRP 0.011 0.001 TRP A 247 HIS 0.003 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00672 ( 4553) covalent geometry : angle 0.74249 ( 6186) hydrogen bonds : bond 0.11955 ( 277) hydrogen bonds : angle 5.42258 ( 795) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.113 Fit side-chains REVERT: A 114 PRO cc_start: 0.7985 (Cg_exo) cc_final: 0.7612 (Cg_exo) REVERT: B 629 GLU cc_start: 0.8387 (tt0) cc_final: 0.8178 (tt0) outliers start: 5 outliers final: 3 residues processed: 69 average time/residue: 0.7189 time to fit residues: 50.8910 Evaluate side-chains 67 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 462 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.3980 chunk 26 optimal weight: 0.0470 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.124823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.100694 restraints weight = 4014.369| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.10 r_work: 0.2959 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.0628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4553 Z= 0.128 Angle : 0.565 10.203 6186 Z= 0.290 Chirality : 0.040 0.145 698 Planarity : 0.004 0.030 769 Dihedral : 4.917 38.253 612 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.27 % Allowed : 8.65 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.36), residues: 553 helix: 1.75 (0.27), residues: 377 sheet: -2.42 (1.29), residues: 10 loop : 1.23 (0.49), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 637 TYR 0.008 0.001 TYR A 495 PHE 0.019 0.001 PHE A 298 TRP 0.013 0.001 TRP A 247 HIS 0.003 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 4553) covalent geometry : angle 0.56465 ( 6186) hydrogen bonds : bond 0.05526 ( 277) hydrogen bonds : angle 4.77078 ( 795) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.182 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 74 average time/residue: 0.7563 time to fit residues: 57.5679 Evaluate side-chains 68 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 621 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 52 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 0.0980 chunk 19 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.124438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.100413 restraints weight = 3978.504| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.09 r_work: 0.2942 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.0760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4553 Z= 0.134 Angle : 0.538 7.697 6186 Z= 0.280 Chirality : 0.041 0.144 698 Planarity : 0.004 0.033 769 Dihedral : 4.507 38.718 605 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.27 % Allowed : 9.28 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.36), residues: 553 helix: 1.72 (0.27), residues: 378 sheet: -2.47 (1.31), residues: 10 loop : 1.25 (0.49), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 222 TYR 0.011 0.001 TYR A 495 PHE 0.017 0.001 PHE A 298 TRP 0.012 0.001 TRP A 131 HIS 0.003 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 4553) covalent geometry : angle 0.53824 ( 6186) hydrogen bonds : bond 0.05763 ( 277) hydrogen bonds : angle 4.73498 ( 795) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.179 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 69 average time/residue: 0.7367 time to fit residues: 52.2901 Evaluate side-chains 65 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 292 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 10 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 0.0570 chunk 6 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.124825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.100803 restraints weight = 3977.565| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.09 r_work: 0.2953 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4553 Z= 0.127 Angle : 0.525 7.717 6186 Z= 0.272 Chirality : 0.041 0.144 698 Planarity : 0.004 0.033 769 Dihedral : 4.470 38.601 605 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.69 % Allowed : 9.28 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.20 (0.36), residues: 553 helix: 1.75 (0.27), residues: 378 sheet: -2.71 (1.32), residues: 10 loop : 1.30 (0.49), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 637 TYR 0.010 0.001 TYR A 495 PHE 0.016 0.001 PHE A 298 TRP 0.012 0.001 TRP A 247 HIS 0.003 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 4553) covalent geometry : angle 0.52470 ( 6186) hydrogen bonds : bond 0.05477 ( 277) hydrogen bonds : angle 4.65440 ( 795) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.181 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 69 average time/residue: 0.6615 time to fit residues: 47.0606 Evaluate side-chains 65 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 463 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 38 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 29 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 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 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.124158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.099954 restraints weight = 3997.937| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.09 r_work: 0.2926 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4553 Z= 0.139 Angle : 0.552 7.727 6186 Z= 0.287 Chirality : 0.042 0.147 698 Planarity : 0.004 0.035 769 Dihedral : 4.531 39.537 605 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.27 % Allowed : 10.13 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.36), residues: 553 helix: 1.69 (0.27), residues: 378 sheet: -2.82 (1.35), residues: 10 loop : 1.28 (0.49), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 637 TYR 0.011 0.001 TYR A 495 PHE 0.016 0.001 PHE A 534 TRP 0.012 0.001 TRP A 247 HIS 0.003 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 4553) covalent geometry : angle 0.55249 ( 6186) hydrogen bonds : bond 0.05890 ( 277) hydrogen bonds : angle 4.72640 ( 795) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.180 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 68 average time/residue: 0.6910 time to fit residues: 48.4132 Evaluate side-chains 66 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 463 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 14 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 52 optimal weight: 0.0030 chunk 38 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.4980 chunk 18 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.125262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.101184 restraints weight = 4046.224| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.10 r_work: 0.2947 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4553 Z= 0.126 Angle : 0.528 7.728 6186 Z= 0.273 Chirality : 0.041 0.145 698 Planarity : 0.004 0.033 769 Dihedral : 4.460 38.955 605 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.27 % Allowed : 9.92 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.20 (0.36), residues: 553 helix: 1.75 (0.27), residues: 378 sheet: -2.86 (1.34), residues: 10 loop : 1.33 (0.50), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 637 TYR 0.010 0.001 TYR A 495 PHE 0.016 0.001 PHE A 298 TRP 0.013 0.001 TRP A 247 HIS 0.002 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 4553) covalent geometry : angle 0.52812 ( 6186) hydrogen bonds : bond 0.05393 ( 277) hydrogen bonds : angle 4.62145 ( 795) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.131 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 67 average time/residue: 0.6701 time to fit residues: 46.2065 Evaluate side-chains 66 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 463 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 52 optimal weight: 0.0270 chunk 53 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 0.0040 chunk 47 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 overall best weight: 0.3850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.126586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.102674 restraints weight = 4058.614| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.10 r_work: 0.2985 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4553 Z= 0.116 Angle : 0.511 7.557 6186 Z= 0.261 Chirality : 0.040 0.140 698 Planarity : 0.004 0.033 769 Dihedral : 4.416 40.759 605 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.84 % Allowed : 10.13 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.36 (0.36), residues: 553 helix: 1.84 (0.27), residues: 379 sheet: -2.91 (1.34), residues: 10 loop : 1.49 (0.51), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 637 TYR 0.009 0.001 TYR A 495 PHE 0.016 0.001 PHE A 298 TRP 0.013 0.001 TRP A 247 HIS 0.002 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 4553) covalent geometry : angle 0.51069 ( 6186) hydrogen bonds : bond 0.04859 ( 277) hydrogen bonds : angle 4.48863 ( 795) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.146 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 65 average time/residue: 0.6970 time to fit residues: 46.6665 Evaluate side-chains 64 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 463 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 11 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 25 optimal weight: 0.0670 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 39 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.126217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.102236 restraints weight = 4045.032| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.10 r_work: 0.2967 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4553 Z= 0.119 Angle : 0.515 7.466 6186 Z= 0.264 Chirality : 0.040 0.142 698 Planarity : 0.004 0.034 769 Dihedral : 4.405 41.664 605 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.84 % Allowed : 10.34 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.36 (0.36), residues: 553 helix: 1.83 (0.27), residues: 379 sheet: -2.88 (1.33), residues: 10 loop : 1.48 (0.50), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 637 TYR 0.009 0.001 TYR A 293 PHE 0.015 0.001 PHE A 298 TRP 0.012 0.001 TRP A 247 HIS 0.002 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 4553) covalent geometry : angle 0.51472 ( 6186) hydrogen bonds : bond 0.05065 ( 277) hydrogen bonds : angle 4.49912 ( 795) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.184 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 65 average time/residue: 0.7458 time to fit residues: 49.8898 Evaluate side-chains 61 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 463 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 30 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.124820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.100662 restraints weight = 3996.983| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.10 r_work: 0.2938 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4553 Z= 0.132 Angle : 0.548 7.610 6186 Z= 0.282 Chirality : 0.041 0.147 698 Planarity : 0.004 0.035 769 Dihedral : 4.518 42.629 605 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.42 % Allowed : 10.76 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.36), residues: 553 helix: 1.67 (0.27), residues: 384 sheet: -2.85 (1.34), residues: 10 loop : 1.51 (0.51), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 637 TYR 0.011 0.001 TYR A 495 PHE 0.016 0.001 PHE A 298 TRP 0.010 0.001 TRP A 247 HIS 0.003 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 4553) covalent geometry : angle 0.54795 ( 6186) hydrogen bonds : bond 0.05646 ( 277) hydrogen bonds : angle 4.61745 ( 795) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.185 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 63 average time/residue: 0.7773 time to fit residues: 50.3447 Evaluate side-chains 63 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 463 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.124653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.100420 restraints weight = 4019.417| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.10 r_work: 0.2936 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4553 Z= 0.136 Angle : 0.559 7.626 6186 Z= 0.287 Chirality : 0.042 0.150 698 Planarity : 0.004 0.035 769 Dihedral : 4.581 44.170 605 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.63 % Allowed : 11.18 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.13 (0.36), residues: 553 helix: 1.62 (0.27), residues: 384 sheet: -2.80 (1.38), residues: 10 loop : 1.49 (0.51), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 637 TYR 0.011 0.001 TYR A 495 PHE 0.017 0.001 PHE A 298 TRP 0.011 0.001 TRP A 247 HIS 0.003 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 4553) covalent geometry : angle 0.55924 ( 6186) hydrogen bonds : bond 0.05737 ( 277) hydrogen bonds : angle 4.64703 ( 795) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.200 Fit side-chains REVERT: A 257 ASP cc_start: 0.7340 (OUTLIER) cc_final: 0.7024 (m-30) outliers start: 3 outliers final: 2 residues processed: 64 average time/residue: 0.7877 time to fit residues: 51.8162 Evaluate side-chains 64 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 463 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 9 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.124747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.100460 restraints weight = 4032.055| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.12 r_work: 0.2964 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4553 Z= 0.131 Angle : 0.554 8.003 6186 Z= 0.283 Chirality : 0.041 0.145 698 Planarity : 0.004 0.034 769 Dihedral : 4.553 43.410 605 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.63 % Allowed : 11.18 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.16 (0.36), residues: 553 helix: 1.64 (0.27), residues: 384 sheet: -2.80 (1.37), residues: 10 loop : 1.51 (0.51), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 637 TYR 0.010 0.001 TYR A 495 PHE 0.017 0.001 PHE A 298 TRP 0.012 0.001 TRP A 247 HIS 0.003 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 4553) covalent geometry : angle 0.55425 ( 6186) hydrogen bonds : bond 0.05565 ( 277) hydrogen bonds : angle 4.61121 ( 795) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2348.56 seconds wall clock time: 40 minutes 37.54 seconds (2437.54 seconds total)