Starting phenix.real_space_refine on Wed Jul 1 23:45:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9km3_62421/07_2026/9km3_62421.cif Found real_map, /net/cci-nas-00/data/ceres_data/9km3_62421/07_2026/9km3_62421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9km3_62421/07_2026/9km3_62421.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9km3_62421/07_2026/9km3_62421.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9km3_62421/07_2026/9km3_62421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9km3_62421/07_2026/9km3_62421.map" } resolution = 2.9 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= 0.041 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: 6 Type Number sf(0) Gaussians S 36 5.16 5 Cl 1 4.86 5 Na 3 4.78 5 C 2833 2.51 5 N 617 2.21 5 O 695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s 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: 4185 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4146 Classifications: {'peptide': 523} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 492} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 35 Ad-hoc single atom residues: {' NA': 3, ' CL': 1} Unusual residues: {'CLR': 1} Inner-chain residues flagged as termini: ['pdbres="GLY A 805 "'] Classifications: {'peptide': 1, 'undetermined': 1, 'water': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain breaks: 4 Time building chain proxies: 1.12, per 1000 atoms: 0.27 Number of scatterers: 4185 At special positions: 0 Unit cell: (83.3, 65.45, 85.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 36 16.00 Na 3 11.00 O 695 8.00 N 617 7.00 C 2833 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 303 " - pdb=" SG CYS A 312 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.36 Conformation dependent library (CDL) restraints added in 147.1 milliseconds 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 1 sheets defined 76.9% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 191 through 201 Processing helix chain 'A' and resid 202 through 207 removed outlier: 4.036A pdb=" N VAL A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.802A pdb=" N TYR A 211 " --> pdb=" O TRP A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 232 Processing helix chain 'A' and resid 232 through 248 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.997A pdb=" N ALA A 257 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 293 removed outlier: 3.892A pdb=" N GLY A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE A 282 " --> pdb=" O TYR A 278 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER A 293 " --> pdb=" O TYR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 385 through 406 Processing helix chain 'A' and resid 413 through 434 removed outlier: 3.695A pdb=" N THR A 419 " --> pdb=" O TYR A 415 " (cutoff:3.500A) Proline residue: A 421 - end of helix removed outlier: 4.003A pdb=" N THR A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 447 removed outlier: 3.760A pdb=" N GLY A 441 " --> pdb=" O GLY A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 470 Processing helix chain 'A' and resid 475 through 481 Processing helix chain 'A' and resid 489 through 524 Processing helix chain 'A' and resid 526 through 530 removed outlier: 3.582A pdb=" N VAL A 530 " --> pdb=" O ILE A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 547 Proline residue: A 543 - end of helix Processing helix chain 'A' and resid 551 through 586 removed outlier: 3.521A pdb=" N TRP A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP A 569 " --> pdb=" O THR A 565 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR A 570 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE A 586 " --> pdb=" O VAL A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 594 removed outlier: 3.603A pdb=" N HIS A 593 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS A 594 " --> pdb=" O ARG A 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 590 through 594' Processing helix chain 'A' and resid 595 through 609 removed outlier: 4.020A pdb=" N LEU A 599 " --> pdb=" O PRO A 595 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 600 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N CYS A 601 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS A 602 " --> pdb=" O THR A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 613 Processing helix chain 'A' and resid 616 through 628 removed outlier: 4.066A pdb=" N MET A 620 " --> pdb=" O GLY A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 647 Processing helix chain 'A' and resid 649 through 662 removed outlier: 3.663A pdb=" N MET A 660 " --> pdb=" O ASP A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 675 removed outlier: 3.585A pdb=" N LYS A 670 " --> pdb=" O SER A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 691 removed outlier: 3.780A pdb=" N THR A 679 " --> pdb=" O PHE A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 719 removed outlier: 3.610A pdb=" N MET A 707 " --> pdb=" O PRO A 703 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N SER A 717 " --> pdb=" O MET A 713 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL A 718 " --> pdb=" O LEU A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 732 removed outlier: 3.775A pdb=" N VAL A 723 " --> pdb=" O ILE A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 744 Processing sheet with id=AA1, first strand: chain 'A' and resid 696 through 697 262 hydrogen bonds defined for protein. 771 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: 0.58 Time building geometry restraints manager: 0.48 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: 1179 1.34 - 1.46: 1125 1.46 - 1.58: 1957 1.58 - 1.69: 0 1.69 - 1.81: 59 Bond restraints: 4320 Sorted by residual: bond pdb=" C8 CLR A 804 " pdb=" C9 CLR A 804 " ideal model delta sigma weight residual 1.535 1.490 0.045 2.00e-02 2.50e+03 5.08e+00 bond pdb=" C14 CLR A 804 " pdb=" C15 CLR A 804 " ideal model delta sigma weight residual 1.523 1.478 0.045 2.00e-02 2.50e+03 4.99e+00 bond pdb=" C20 CLR A 804 " pdb=" C22 CLR A 804 " ideal model delta sigma weight residual 1.535 1.495 0.040 2.00e-02 2.50e+03 3.93e+00 bond pdb=" C GLU A 365 " pdb=" N TYR A 366 " ideal model delta sigma weight residual 1.331 1.305 0.026 1.40e-02 5.10e+03 3.57e+00 bond pdb=" C3 CLR A 804 " pdb=" C4 CLR A 804 " ideal model delta sigma weight residual 1.526 1.561 -0.035 2.00e-02 2.50e+03 3.12e+00 ... (remaining 4315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 5854 3.13 - 6.26: 34 6.26 - 9.40: 6 9.40 - 12.53: 7 12.53 - 15.66: 3 Bond angle restraints: 5904 Sorted by residual: angle pdb=" C12 CLR A 804 " pdb=" C13 CLR A 804 " pdb=" C17 CLR A 804 " ideal model delta sigma weight residual 116.52 100.86 15.66 3.00e+00 1.11e-01 2.72e+01 angle pdb=" C14 CLR A 804 " pdb=" C13 CLR A 804 " pdb=" C18 CLR A 804 " ideal model delta sigma weight residual 112.24 127.55 -15.31 3.00e+00 1.11e-01 2.61e+01 angle pdb=" C4 CLR A 804 " pdb=" C5 CLR A 804 " pdb=" C6 CLR A 804 " ideal model delta sigma weight residual 120.33 133.03 -12.70 3.00e+00 1.11e-01 1.79e+01 angle pdb=" C16 CLR A 804 " pdb=" C17 CLR A 804 " pdb=" C20 CLR A 804 " ideal model delta sigma weight residual 112.02 124.33 -12.31 3.00e+00 1.11e-01 1.68e+01 angle pdb=" C1 CLR A 804 " pdb=" C10 CLR A 804 " pdb=" C9 CLR A 804 " ideal model delta sigma weight residual 108.36 96.50 11.86 3.00e+00 1.11e-01 1.56e+01 ... (remaining 5899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.64: 2226 21.64 - 43.28: 216 43.28 - 64.91: 56 64.91 - 86.55: 3 86.55 - 108.19: 4 Dihedral angle restraints: 2505 sinusoidal: 985 harmonic: 1520 Sorted by residual: dihedral pdb=" CA GLU A 365 " pdb=" C GLU A 365 " pdb=" N TYR A 366 " pdb=" CA TYR A 366 " ideal model delta harmonic sigma weight residual 180.00 156.15 23.85 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" C10 CLR A 804 " pdb=" C1 CLR A 804 " pdb=" C2 CLR A 804 " pdb=" C3 CLR A 804 " ideal model delta sinusoidal sigma weight residual -56.83 51.36 -108.19 1 3.00e+01 1.11e-03 1.40e+01 dihedral pdb=" C1 CLR A 804 " pdb=" C2 CLR A 804 " pdb=" C3 CLR A 804 " pdb=" O1 CLR A 804 " ideal model delta sinusoidal sigma weight residual 180.04 72.52 107.52 1 3.00e+01 1.11e-03 1.39e+01 ... (remaining 2502 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 660 0.112 - 0.223: 6 0.223 - 0.335: 1 0.335 - 0.447: 1 0.447 - 0.559: 1 Chirality restraints: 669 Sorted by residual: chirality pdb=" C20 CLR A 804 " pdb=" C17 CLR A 804 " pdb=" C21 CLR A 804 " pdb=" C22 CLR A 804 " both_signs ideal model delta sigma weight residual False 2.59 2.03 0.56 2.00e-01 2.50e+01 7.80e+00 chirality pdb=" C9 CLR A 804 " pdb=" C10 CLR A 804 " pdb=" C11 CLR A 804 " pdb=" C8 CLR A 804 " both_signs ideal model delta sigma weight residual False -2.45 -2.80 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" C13 CLR A 804 " pdb=" C12 CLR A 804 " pdb=" C14 CLR A 804 " pdb=" C17 CLR A 804 " both_signs ideal model delta sigma weight residual False -2.93 -3.18 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 666 not shown) Planarity restraints: 703 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 258 " 0.044 5.00e-02 4.00e+02 6.72e-02 7.22e+00 pdb=" N PRO A 259 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 259 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 259 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 366 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" C TYR A 366 " 0.028 2.00e-02 2.50e+03 pdb=" O TYR A 366 " -0.010 2.00e-02 2.50e+03 pdb=" N PHE A 367 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 610 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO A 611 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 611 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 611 " 0.018 5.00e-02 4.00e+02 ... (remaining 700 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 723 2.76 - 3.29: 3890 3.29 - 3.83: 6900 3.83 - 4.36: 7640 4.36 - 4.90: 14053 Nonbonded interactions: 33206 Sorted by model distance: nonbonded pdb=" OE1 GLU A 640 " pdb="NA NA A 808 " model vdw 2.225 3.210 nonbonded pdb=" OD1 ASN A 205 " pdb="NA NA A 806 " model vdw 2.320 3.210 nonbonded pdb=" O VAL A 201 " pdb="NA NA A 807 " model vdw 2.326 3.210 nonbonded pdb=" OG1 THR A 570 " pdb="NA NA A 807 " model vdw 2.334 3.210 nonbonded pdb=" OE2 GLU A 240 " pdb="NA NA A 808 " model vdw 2.337 3.210 ... (remaining 33201 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.120 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.680 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 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 : 0.003 0.045 4321 Z= 0.162 Angle : 0.796 15.659 5906 Z= 0.350 Chirality : 0.050 0.559 669 Planarity : 0.005 0.067 703 Dihedral : 17.891 108.188 1530 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.68 % Allowed : 27.03 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.16 (0.38), residues: 519 helix: 1.81 (0.28), residues: 358 sheet: None (None), residues: 0 loop : -1.71 (0.46), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 652 TYR 0.020 0.001 TYR A 278 PHE 0.021 0.001 PHE A 572 TRP 0.009 0.001 TRP A 705 HIS 0.000 0.000 HIS A 521 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 ( 4320) covalent geometry : angle 0.79654 / 0.35 ( 5904) SS BOND : bond 0.00102 / 0.05 ( 1) SS BOND : angle 0.49430 / 0.27 ( 2) hydrogen bonds : bond 0.14578 / 9.97 ( 262) hydrogen bonds : angle 5.26833 / 3.67 ( 771) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.152 Fit side-chains REVERT: A 249 GLN cc_start: 0.7550 (mt0) cc_final: 0.7130 (mt0) REVERT: A 544 GLU cc_start: 0.7345 (tp30) cc_final: 0.7133 (tp30) outliers start: 3 outliers final: 2 residues processed: 79 average time/residue: 0.3541 time to fit residues: 29.5094 Evaluate side-chains 66 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 632 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 ASN A 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.152538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.125758 restraints weight = 5179.804| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.16 r_work: 0.3339 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4321 Z= 0.135 Angle : 0.559 6.110 5906 Z= 0.285 Chirality : 0.042 0.130 669 Planarity : 0.004 0.047 703 Dihedral : 10.529 99.538 624 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.38 % Allowed : 24.10 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.38 (0.38), residues: 519 helix: 1.94 (0.28), residues: 368 sheet: None (None), residues: 0 loop : -1.80 (0.49), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 385 TYR 0.019 0.001 TYR A 278 PHE 0.015 0.001 PHE A 687 TRP 0.010 0.001 TRP A 705 HIS 0.001 0.001 HIS A 701 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 4320) covalent geometry : angle 0.55849 / 0.28 ( 5904) SS BOND : bond 0.00314 / 0.17 ( 1) SS BOND : angle 0.91629 / 0.50 ( 2) hydrogen bonds : bond 0.05806 / 3.88 ( 262) hydrogen bonds : angle 4.03072 / 2.79 ( 771) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.150 Fit side-chains REVERT: A 249 GLN cc_start: 0.7489 (mt0) cc_final: 0.7056 (mt0) outliers start: 15 outliers final: 5 residues processed: 76 average time/residue: 0.3490 time to fit residues: 27.9763 Evaluate side-chains 72 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 590 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.149860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.122652 restraints weight = 5111.304| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.29 r_work: 0.3318 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4321 Z= 0.128 Angle : 0.556 7.268 5906 Z= 0.278 Chirality : 0.042 0.131 669 Planarity : 0.004 0.039 703 Dihedral : 8.732 82.644 623 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.15 % Allowed : 23.42 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.39), residues: 519 helix: 2.02 (0.28), residues: 369 sheet: None (None), residues: 0 loop : -1.80 (0.48), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 208 TYR 0.020 0.001 TYR A 278 PHE 0.014 0.001 PHE A 687 TRP 0.008 0.001 TRP A 255 HIS 0.002 0.001 HIS A 701 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 4320) covalent geometry : angle 0.55603 / 0.28 ( 5904) SS BOND : bond 0.00242 / 0.13 ( 1) SS BOND : angle 0.99235 / 0.55 ( 2) hydrogen bonds : bond 0.05638 / 3.78 ( 262) hydrogen bonds : angle 3.92784 / 2.71 ( 771) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.147 Fit side-chains REVERT: A 249 GLN cc_start: 0.7061 (mt0) cc_final: 0.6768 (mt0) REVERT: A 383 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6885 (mt-10) REVERT: A 585 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6344 (mp0) outliers start: 14 outliers final: 6 residues processed: 72 average time/residue: 0.3662 time to fit residues: 27.8011 Evaluate side-chains 72 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 585 GLU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 623 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 2 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.152546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.127161 restraints weight = 5279.245| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.06 r_work: 0.3354 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4321 Z= 0.136 Angle : 0.569 7.612 5906 Z= 0.286 Chirality : 0.043 0.136 669 Planarity : 0.004 0.034 703 Dihedral : 7.952 76.636 623 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.05 % Allowed : 22.07 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.38 (0.38), residues: 519 helix: 1.99 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.83 (0.46), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 548 TYR 0.021 0.001 TYR A 278 PHE 0.020 0.001 PHE A 586 TRP 0.008 0.001 TRP A 255 HIS 0.002 0.001 HIS A 701 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 4320) covalent geometry : angle 0.56857 / 0.29 ( 5904) SS BOND : bond 0.00199 / 0.10 ( 1) SS BOND : angle 1.02624 / 0.57 ( 2) hydrogen bonds : bond 0.05957 / 3.99 ( 262) hydrogen bonds : angle 3.93234 / 2.71 ( 771) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.158 Fit side-chains REVERT: A 585 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.6654 (mp0) REVERT: A 729 MET cc_start: 0.7535 (tpp) cc_final: 0.7324 (mmp) outliers start: 18 outliers final: 7 residues processed: 74 average time/residue: 0.3332 time to fit residues: 26.1275 Evaluate side-chains 72 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 585 GLU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 623 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 47 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 0.0370 chunk 51 optimal weight: 8.9990 chunk 32 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.148667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.121892 restraints weight = 5145.241| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.33 r_work: 0.3260 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4321 Z= 0.120 Angle : 0.540 7.981 5906 Z= 0.272 Chirality : 0.042 0.180 669 Planarity : 0.004 0.033 703 Dihedral : 5.143 52.096 623 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.15 % Allowed : 22.97 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.50 (0.38), residues: 519 helix: 2.10 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.82 (0.46), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 591 TYR 0.019 0.001 TYR A 278 PHE 0.014 0.001 PHE A 687 TRP 0.009 0.001 TRP A 255 HIS 0.001 0.001 HIS A 521 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 4320) covalent geometry : angle 0.53972 / 0.27 ( 5904) SS BOND : bond 0.00196 / 0.10 ( 1) SS BOND : angle 0.95922 / 0.53 ( 2) hydrogen bonds : bond 0.05376 / 3.61 ( 262) hydrogen bonds : angle 3.84462 / 2.65 ( 771) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.149 Fit side-chains REVERT: A 585 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6283 (mp0) outliers start: 14 outliers final: 3 residues processed: 74 average time/residue: 0.3594 time to fit residues: 28.0874 Evaluate side-chains 67 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 585 GLU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 614 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 29 optimal weight: 0.0040 chunk 22 optimal weight: 0.9990 chunk 18 optimal weight: 0.0020 overall best weight: 0.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.156903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.131590 restraints weight = 5304.246| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.13 r_work: 0.3412 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4321 Z= 0.110 Angle : 0.517 8.870 5906 Z= 0.262 Chirality : 0.041 0.195 669 Planarity : 0.004 0.030 703 Dihedral : 4.863 58.374 623 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.60 % Allowed : 22.75 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.58 (0.38), residues: 519 helix: 2.15 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.78 (0.47), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 652 TYR 0.017 0.001 TYR A 278 PHE 0.014 0.001 PHE A 687 TRP 0.008 0.001 TRP A 255 HIS 0.001 0.000 HIS A 521 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 ( 4320) covalent geometry : angle 0.51667 / 0.26 ( 5904) SS BOND : bond 0.00260 / 0.14 ( 1) SS BOND : angle 0.96738 / 0.55 ( 2) hydrogen bonds : bond 0.04754 / 3.16 ( 262) hydrogen bonds : angle 3.76510 / 2.60 ( 771) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.125 Fit side-chains REVERT: A 729 MET cc_start: 0.7411 (tpp) cc_final: 0.7136 (mmp) outliers start: 16 outliers final: 9 residues processed: 74 average time/residue: 0.3094 time to fit residues: 24.2969 Evaluate side-chains 71 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 718 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 23 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 46 optimal weight: 0.0050 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 0.0000 chunk 31 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 51 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.152014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.126069 restraints weight = 5181.900| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.22 r_work: 0.3377 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 4321 Z= 0.110 Angle : 0.530 9.044 5906 Z= 0.265 Chirality : 0.042 0.200 669 Planarity : 0.004 0.030 703 Dihedral : 4.585 49.687 623 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.48 % Allowed : 25.23 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.67 (0.39), residues: 519 helix: 2.20 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.69 (0.47), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 591 TYR 0.016 0.001 TYR A 278 PHE 0.015 0.001 PHE A 687 TRP 0.009 0.001 TRP A 255 HIS 0.001 0.000 HIS A 521 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 4320) covalent geometry : angle 0.53002 / 0.26 ( 5904) SS BOND : bond 0.00188 / 0.10 ( 1) SS BOND : angle 0.81199 / 0.46 ( 2) hydrogen bonds : bond 0.04679 / 3.10 ( 262) hydrogen bonds : angle 3.73607 / 2.58 ( 771) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.160 Fit side-chains REVERT: A 371 MET cc_start: 0.8689 (ttp) cc_final: 0.8471 (tmm) outliers start: 11 outliers final: 8 residues processed: 72 average time/residue: 0.3045 time to fit residues: 23.2276 Evaluate side-chains 70 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 718 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 2 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 25 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 46 optimal weight: 0.0170 chunk 18 optimal weight: 1.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.156068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.130823 restraints weight = 5178.777| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.10 r_work: 0.3401 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4321 Z= 0.119 Angle : 0.542 9.817 5906 Z= 0.277 Chirality : 0.042 0.177 669 Planarity : 0.004 0.029 703 Dihedral : 4.489 41.249 623 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.70 % Allowed : 25.00 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.58 (0.38), residues: 519 helix: 2.15 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.75 (0.47), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 548 TYR 0.018 0.001 TYR A 278 PHE 0.017 0.001 PHE A 687 TRP 0.008 0.001 TRP A 255 HIS 0.001 0.000 HIS A 701 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 4320) covalent geometry : angle 0.54224 / 0.28 ( 5904) SS BOND : bond 0.00366 / 0.19 ( 1) SS BOND : angle 0.99959 / 0.55 ( 2) hydrogen bonds : bond 0.05010 / 3.32 ( 262) hydrogen bonds : angle 3.75759 / 2.60 ( 771) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.150 Fit side-chains REVERT: A 729 MET cc_start: 0.7415 (tpp) cc_final: 0.7088 (mmp) outliers start: 12 outliers final: 8 residues processed: 72 average time/residue: 0.3266 time to fit residues: 24.9179 Evaluate side-chains 71 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 718 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 23 optimal weight: 0.3980 chunk 2 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 0.0980 chunk 46 optimal weight: 0.0060 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.153924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.127644 restraints weight = 5189.360| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.32 r_work: 0.3383 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 4321 Z= 0.109 Angle : 0.539 9.432 5906 Z= 0.269 Chirality : 0.041 0.174 669 Planarity : 0.004 0.030 703 Dihedral : 4.171 31.084 623 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.03 % Allowed : 26.35 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.38), residues: 519 helix: 2.22 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.66 (0.47), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 591 TYR 0.018 0.001 TYR A 278 PHE 0.036 0.001 PHE A 572 TRP 0.009 0.001 TRP A 255 HIS 0.001 0.000 HIS A 521 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 ( 4320) covalent geometry : angle 0.53899 / 0.27 ( 5904) SS BOND : bond 0.00045 / 0.02 ( 1) SS BOND : angle 0.65400 / 0.37 ( 2) hydrogen bonds : bond 0.04453 / 2.95 ( 262) hydrogen bonds : angle 3.69547 / 2.56 ( 771) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.148 Fit side-chains REVERT: A 510 PHE cc_start: 0.6306 (OUTLIER) cc_final: 0.5392 (t80) REVERT: A 729 MET cc_start: 0.7150 (tpp) cc_final: 0.6873 (mmp) outliers start: 9 outliers final: 5 residues processed: 68 average time/residue: 0.3151 time to fit residues: 22.7914 Evaluate side-chains 69 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 718 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 20 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 18 optimal weight: 0.4980 chunk 38 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 chunk 13 optimal weight: 0.1980 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.156643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.131794 restraints weight = 5217.011| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.08 r_work: 0.3411 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4321 Z= 0.121 Angle : 0.548 8.469 5906 Z= 0.282 Chirality : 0.042 0.167 669 Planarity : 0.004 0.029 703 Dihedral : 4.228 34.035 623 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.80 % Allowed : 26.58 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.64 (0.38), residues: 519 helix: 2.17 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.68 (0.47), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 548 TYR 0.018 0.001 TYR A 278 PHE 0.018 0.001 PHE A 687 TRP 0.008 0.001 TRP A 255 HIS 0.001 0.000 HIS A 701 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 4320) covalent geometry : angle 0.54811 / 0.28 ( 5904) SS BOND : bond 0.00142 / 0.07 ( 1) SS BOND : angle 0.77135 / 0.42 ( 2) hydrogen bonds : bond 0.04945 / 3.26 ( 262) hydrogen bonds : angle 3.72345 / 2.58 ( 771) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.213 Fit side-chains REVERT: A 729 MET cc_start: 0.7438 (tpp) cc_final: 0.7184 (mmp) outliers start: 8 outliers final: 5 residues processed: 68 average time/residue: 0.3287 time to fit residues: 23.8543 Evaluate side-chains 68 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 718 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 47 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 40 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.146917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.120081 restraints weight = 5219.471| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.31 r_work: 0.3306 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 4321 Z= 0.144 Angle : 0.593 9.460 5906 Z= 0.301 Chirality : 0.044 0.166 669 Planarity : 0.004 0.029 703 Dihedral : 4.235 23.979 622 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.25 % Allowed : 26.58 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.44 (0.38), residues: 519 helix: 2.02 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.75 (0.47), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 591 TYR 0.021 0.001 TYR A 278 PHE 0.031 0.002 PHE A 572 TRP 0.009 0.001 TRP A 255 HIS 0.002 0.001 HIS A 701 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 4320) covalent geometry : angle 0.59315 / 0.30 ( 5904) SS BOND : bond 0.00169 / 0.09 ( 1) SS BOND : angle 1.11082 / 0.61 ( 2) hydrogen bonds : bond 0.06042 / 4.03 ( 262) hydrogen bonds : angle 3.84473 / 2.65 ( 771) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1461.78 seconds wall clock time: 25 minutes 38.61 seconds (1538.61 seconds total)