Starting phenix.real_space_refine on Fri Aug 22 14:01:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7soc_25266/08_2025/7soc_25266.cif Found real_map, /net/cci-nas-00/data/ceres_data/7soc_25266/08_2025/7soc_25266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7soc_25266/08_2025/7soc_25266.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7soc_25266/08_2025/7soc_25266.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7soc_25266/08_2025/7soc_25266.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7soc_25266/08_2025/7soc_25266.map" } resolution = 3.3 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= -0.002 sd= 0.071 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 16 5.16 5 C 2176 2.51 5 N 577 2.21 5 O 679 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 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: 3448 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1589 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 12, 'TRANS': 187} Chain: "H" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 996 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "L" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 778 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Chain: "B" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 0.95, per 1000 atoms: 0.28 Number of scatterers: 3448 At special positions: 0 Unit cell: (91.887, 78.399, 82.614, 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 16 16.00 O 679 8.00 N 577 7.00 C 2176 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.10 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.07 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.07 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 Links applied ALPHA1-3 " BMA B 3 " - " MAN B 4 " ALPHA1-6 " BMA B 3 " - " MAN B 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " BETA1-6 " NAG B 1 " - " FUC B 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG B 1 " - " ASN A 343 " Time building additional restraints: 0.29 Conformation dependent library (CDL) restraints added in 120.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 782 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 9 sheets defined 10.9% alpha, 30.5% 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 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.841A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.621A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.152A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.006A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.658A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.604A pdb=" N GLY H 33 " --> pdb=" O ASP H 99 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.803A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 11 116 hydrogen bonds defined for protein. 261 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: 0.49 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 930 1.33 - 1.46: 914 1.46 - 1.58: 1671 1.58 - 1.71: 0 1.71 - 1.84: 19 Bond restraints: 3534 Sorted by residual: bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.413 1.475 -0.062 2.00e-02 2.50e+03 9.50e+00 bond pdb=" C5 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.413 1.465 -0.052 2.00e-02 2.50e+03 6.79e+00 bond pdb=" C5 MAN B 4 " pdb=" O5 MAN B 4 " ideal model delta sigma weight residual 1.418 1.469 -0.051 2.00e-02 2.50e+03 6.57e+00 bond pdb=" C5 MAN B 5 " pdb=" O5 MAN B 5 " ideal model delta sigma weight residual 1.418 1.469 -0.051 2.00e-02 2.50e+03 6.50e+00 bond pdb=" N ASP H 115 " pdb=" CA ASP H 115 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.37e+00 ... (remaining 3529 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 4088 1.51 - 3.02: 584 3.02 - 4.53: 79 4.53 - 6.04: 34 6.04 - 7.55: 19 Bond angle restraints: 4804 Sorted by residual: angle pdb=" C PHE A 490 " pdb=" N PRO A 491 " pdb=" CA PRO A 491 " ideal model delta sigma weight residual 119.56 126.74 -7.18 1.02e+00 9.61e-01 4.95e+01 angle pdb=" C ILE L 59 " pdb=" N PRO L 60 " pdb=" CA PRO L 60 " ideal model delta sigma weight residual 119.89 126.97 -7.08 1.02e+00 9.61e-01 4.82e+01 angle pdb=" C LEU A 425 " pdb=" N PRO A 426 " pdb=" CA PRO A 426 " ideal model delta sigma weight residual 119.85 126.82 -6.97 1.01e+00 9.80e-01 4.76e+01 angle pdb=" C GLN A 498 " pdb=" N PRO A 499 " pdb=" CA PRO A 499 " ideal model delta sigma weight residual 119.56 126.57 -7.01 1.02e+00 9.61e-01 4.72e+01 angle pdb=" C THR A 478 " pdb=" N PRO A 479 " pdb=" CA PRO A 479 " ideal model delta sigma weight residual 119.78 126.73 -6.95 1.03e+00 9.43e-01 4.55e+01 ... (remaining 4799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.66: 2076 21.66 - 43.32: 54 43.32 - 64.97: 12 64.97 - 86.63: 12 86.63 - 108.29: 4 Dihedral angle restraints: 2158 sinusoidal: 919 harmonic: 1239 Sorted by residual: dihedral pdb=" O4 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.58 108.29 1 3.00e+01 1.11e-03 1.40e+01 dihedral pdb=" C3 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual 47.62 -59.62 107.24 1 3.00e+01 1.11e-03 1.38e+01 dihedral pdb=" C6 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O4 BMA B 3 " ideal model delta sinusoidal sigma weight residual -163.34 -61.42 -101.92 1 3.00e+01 1.11e-03 1.29e+01 ... (remaining 2155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 414 0.075 - 0.150: 95 0.150 - 0.225: 21 0.225 - 0.299: 3 0.299 - 0.374: 3 Chirality restraints: 536 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.01e+02 chirality pdb=" C1 BMA B 3 " pdb=" O4 NAG B 2 " pdb=" C2 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.16e+01 chirality pdb=" C1 MAN B 4 " pdb=" O3 BMA B 3 " pdb=" C2 MAN B 4 " pdb=" O5 MAN B 4 " both_signs ideal model delta sigma weight residual False 2.40 2.46 -0.06 2.00e-02 2.50e+03 9.33e+00 ... (remaining 533 not shown) Planarity restraints: 614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY H 113 " 0.015 2.00e-02 2.50e+03 2.93e-02 8.59e+00 pdb=" C GLY H 113 " -0.051 2.00e-02 2.50e+03 pdb=" O GLY H 113 " 0.019 2.00e-02 2.50e+03 pdb=" N PHE H 114 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.023 2.00e-02 2.50e+03 2.30e-02 6.62e+00 pdb=" CG ASN A 331 " 0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.034 2.00e-02 2.50e+03 pdb=" C1 NAG A1301 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 382 " -0.010 2.00e-02 2.50e+03 2.08e-02 4.31e+00 pdb=" C VAL A 382 " 0.036 2.00e-02 2.50e+03 pdb=" O VAL A 382 " -0.014 2.00e-02 2.50e+03 pdb=" N CYS A 383 " -0.012 2.00e-02 2.50e+03 ... (remaining 611 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 1858 3.00 - 3.48: 2935 3.48 - 3.95: 5779 3.95 - 4.43: 6532 4.43 - 4.90: 10740 Nonbonded interactions: 27844 Sorted by model distance: nonbonded pdb=" N ASP H 115 " pdb=" OD1 ASP H 115 " model vdw 2.526 3.120 nonbonded pdb=" N ASP L 61 " pdb=" OD1 ASP L 61 " model vdw 2.528 3.120 nonbonded pdb=" N ASP A 428 " pdb=" OD1 ASP A 428 " model vdw 2.592 3.120 nonbonded pdb=" N ASP H 89 " pdb=" OD1 ASP H 89 " model vdw 2.598 3.120 nonbonded pdb=" N GLU L 80 " pdb=" O GLU L 80 " model vdw 2.607 2.496 ... (remaining 27839 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: 10.050 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.310 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 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 : 0.011 0.070 3547 Z= 0.613 Angle : 1.235 7.554 4837 Z= 0.816 Chirality : 0.072 0.374 536 Planarity : 0.005 0.029 612 Dihedral : 13.133 108.287 1358 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 0.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.39), residues: 427 helix: -4.85 (0.23), residues: 27 sheet: 0.86 (0.41), residues: 154 loop : 0.50 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 509 TYR 0.023 0.003 TYR A 495 PHE 0.032 0.003 PHE A 329 TRP 0.020 0.004 TRP H 50 HIS 0.002 0.001 HIS L 92 Details of bonding type rmsd covalent geometry : bond 0.01090 ( 3534) covalent geometry : angle 1.22105 ( 4804) SS BOND : bond 0.03812 ( 6) SS BOND : angle 3.15232 ( 12) hydrogen bonds : bond 0.16523 ( 113) hydrogen bonds : angle 8.98908 ( 261) link_ALPHA1-3 : bond 0.06203 ( 1) link_ALPHA1-3 : angle 2.04188 ( 3) link_ALPHA1-6 : bond 0.05231 ( 1) link_ALPHA1-6 : angle 2.56792 ( 3) link_BETA1-4 : bond 0.06420 ( 2) link_BETA1-4 : angle 2.17920 ( 6) link_BETA1-6 : bond 0.04396 ( 1) link_BETA1-6 : angle 1.49948 ( 3) link_NAG-ASN : bond 0.05479 ( 2) link_NAG-ASN : angle 1.92623 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.111 Fit side-chains REVERT: A 340 GLU cc_start: 0.8715 (pt0) cc_final: 0.8477 (pt0) REVERT: A 378 LYS cc_start: 0.8603 (mttt) cc_final: 0.8141 (mtmt) REVERT: A 406 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7994 (mt-10) REVERT: A 517 LEU cc_start: 0.6915 (tp) cc_final: 0.6336 (tp) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0633 time to fit residues: 4.3656 Evaluate side-chains 35 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.3980 chunk 32 optimal weight: 0.0870 chunk 31 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.4980 chunk 30 optimal weight: 0.0980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.3158 ------------------------------------------------------------------------------- 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 = 0.3139 r_free = 0.3139 target = 0.112585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.098666 restraints weight = 4196.292| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.29 r_work: 0.2859 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3547 Z= 0.137 Angle : 0.526 5.229 4837 Z= 0.277 Chirality : 0.046 0.193 536 Planarity : 0.004 0.032 612 Dihedral : 10.384 85.631 617 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.38 % Allowed : 4.96 % Favored : 93.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.40), residues: 427 helix: -4.32 (0.45), residues: 27 sheet: 0.73 (0.40), residues: 159 loop : 0.70 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 67 TYR 0.018 0.001 TYR A 495 PHE 0.019 0.002 PHE A 515 TRP 0.011 0.001 TRP A 436 HIS 0.003 0.001 HIS L 92 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 3534) covalent geometry : angle 0.50961 ( 4804) SS BOND : bond 0.00530 ( 6) SS BOND : angle 1.01935 ( 12) hydrogen bonds : bond 0.04010 ( 113) hydrogen bonds : angle 7.09624 ( 261) link_ALPHA1-3 : bond 0.01261 ( 1) link_ALPHA1-3 : angle 2.35559 ( 3) link_ALPHA1-6 : bond 0.01075 ( 1) link_ALPHA1-6 : angle 1.39646 ( 3) link_BETA1-4 : bond 0.00695 ( 2) link_BETA1-4 : angle 2.26576 ( 6) link_BETA1-6 : bond 0.00220 ( 1) link_BETA1-6 : angle 1.28670 ( 3) link_NAG-ASN : bond 0.00812 ( 2) link_NAG-ASN : angle 1.77635 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.112 Fit side-chains REVERT: A 340 GLU cc_start: 0.8788 (pt0) cc_final: 0.8567 (pt0) REVERT: A 378 LYS cc_start: 0.8778 (mttt) cc_final: 0.8017 (mtmt) REVERT: A 471 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7997 (mt-10) REVERT: H 102 ARG cc_start: 0.9293 (ttm-80) cc_final: 0.8903 (ttm-80) outliers start: 5 outliers final: 3 residues processed: 40 average time/residue: 0.0376 time to fit residues: 2.0292 Evaluate side-chains 34 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain H residue 69 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 32 optimal weight: 0.0980 chunk 20 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3112 r_free = 0.3112 target = 0.110237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.095419 restraints weight = 4208.288| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 1.38 r_work: 0.2809 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 3547 Z= 0.204 Angle : 0.551 6.201 4837 Z= 0.287 Chirality : 0.047 0.219 536 Planarity : 0.005 0.035 612 Dihedral : 9.277 75.822 617 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.65 % Allowed : 6.06 % Favored : 92.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.40), residues: 427 helix: -4.11 (0.56), residues: 27 sheet: 0.55 (0.40), residues: 159 loop : 0.54 (0.41), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 67 TYR 0.025 0.002 TYR A 495 PHE 0.015 0.002 PHE A 429 TRP 0.010 0.002 TRP A 436 HIS 0.003 0.001 HIS L 92 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 3534) covalent geometry : angle 0.54070 ( 4804) SS BOND : bond 0.00441 ( 6) SS BOND : angle 0.96250 ( 12) hydrogen bonds : bond 0.03997 ( 113) hydrogen bonds : angle 6.77179 ( 261) link_ALPHA1-3 : bond 0.00986 ( 1) link_ALPHA1-3 : angle 1.10408 ( 3) link_ALPHA1-6 : bond 0.01203 ( 1) link_ALPHA1-6 : angle 1.09759 ( 3) link_BETA1-4 : bond 0.00671 ( 2) link_BETA1-4 : angle 1.81990 ( 6) link_BETA1-6 : bond 0.00537 ( 1) link_BETA1-6 : angle 1.28372 ( 3) link_NAG-ASN : bond 0.00579 ( 2) link_NAG-ASN : angle 1.79952 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.131 Fit side-chains REVERT: A 378 LYS cc_start: 0.8835 (mttt) cc_final: 0.8078 (mtmt) REVERT: A 471 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8190 (mt-10) outliers start: 6 outliers final: 5 residues processed: 38 average time/residue: 0.0438 time to fit residues: 2.3760 Evaluate side-chains 34 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain L residue 7 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 0.2980 chunk 5 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 20 optimal weight: 0.0060 chunk 40 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 41 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.111173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.096584 restraints weight = 4103.016| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.36 r_work: 0.2826 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3547 Z= 0.147 Angle : 0.518 7.848 4837 Z= 0.259 Chirality : 0.046 0.286 536 Planarity : 0.004 0.038 612 Dihedral : 8.471 67.610 617 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.10 % Allowed : 7.44 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.41), residues: 427 helix: -4.01 (0.64), residues: 27 sheet: 0.52 (0.40), residues: 158 loop : 0.52 (0.42), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 67 TYR 0.015 0.001 TYR A 495 PHE 0.007 0.001 PHE L 84 TRP 0.008 0.001 TRP H 47 HIS 0.003 0.001 HIS L 92 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 3534) covalent geometry : angle 0.49349 ( 4804) SS BOND : bond 0.00315 ( 6) SS BOND : angle 0.70286 ( 12) hydrogen bonds : bond 0.03410 ( 113) hydrogen bonds : angle 6.50557 ( 261) link_ALPHA1-3 : bond 0.01285 ( 1) link_ALPHA1-3 : angle 1.38472 ( 3) link_ALPHA1-6 : bond 0.01337 ( 1) link_ALPHA1-6 : angle 1.54480 ( 3) link_BETA1-4 : bond 0.00591 ( 2) link_BETA1-4 : angle 1.67423 ( 6) link_BETA1-6 : bond 0.00219 ( 1) link_BETA1-6 : angle 1.18589 ( 3) link_NAG-ASN : bond 0.01328 ( 2) link_NAG-ASN : angle 3.82717 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.094 Fit side-chains REVERT: A 378 LYS cc_start: 0.8819 (mttt) cc_final: 0.8138 (mtmt) REVERT: A 471 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8194 (mt-10) outliers start: 4 outliers final: 3 residues processed: 28 average time/residue: 0.0408 time to fit residues: 1.6663 Evaluate side-chains 29 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain L residue 61 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 15 optimal weight: 0.0040 chunk 22 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 overall best weight: 0.5192 ------------------------------------------------------------------------------- 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 = 0.3103 r_free = 0.3103 target = 0.109844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.095152 restraints weight = 4155.256| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.35 r_work: 0.2802 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 3547 Z= 0.177 Angle : 0.549 8.724 4837 Z= 0.271 Chirality : 0.046 0.255 536 Planarity : 0.004 0.038 612 Dihedral : 6.666 52.119 617 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.20 % Allowed : 6.89 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.41), residues: 427 helix: -3.98 (0.66), residues: 27 sheet: 0.37 (0.41), residues: 157 loop : 0.36 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 67 TYR 0.017 0.002 TYR A 495 PHE 0.010 0.001 PHE L 84 TRP 0.010 0.001 TRP H 47 HIS 0.004 0.001 HIS L 92 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 3534) covalent geometry : angle 0.51678 ( 4804) SS BOND : bond 0.00347 ( 6) SS BOND : angle 0.77476 ( 12) hydrogen bonds : bond 0.03445 ( 113) hydrogen bonds : angle 6.45330 ( 261) link_ALPHA1-3 : bond 0.01328 ( 1) link_ALPHA1-3 : angle 1.03377 ( 3) link_ALPHA1-6 : bond 0.01091 ( 1) link_ALPHA1-6 : angle 2.16259 ( 3) link_BETA1-4 : bond 0.00610 ( 2) link_BETA1-4 : angle 1.70772 ( 6) link_BETA1-6 : bond 0.00198 ( 1) link_BETA1-6 : angle 1.21412 ( 3) link_NAG-ASN : bond 0.01107 ( 2) link_NAG-ASN : angle 4.63078 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.144 Fit side-chains REVERT: A 378 LYS cc_start: 0.8814 (mttt) cc_final: 0.8135 (mtmt) REVERT: A 471 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8174 (mt-10) REVERT: H 43 GLN cc_start: 0.8620 (mm110) cc_final: 0.8332 (mp10) REVERT: H 70 MET cc_start: 0.9313 (mtt) cc_final: 0.8683 (mtt) REVERT: L 82 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7961 (pm20) outliers start: 8 outliers final: 7 residues processed: 36 average time/residue: 0.0431 time to fit residues: 2.2145 Evaluate side-chains 38 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 82 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3116 r_free = 0.3116 target = 0.110776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.093840 restraints weight = 4052.685| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.57 r_work: 0.2789 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 3547 Z= 0.219 Angle : 0.566 8.240 4837 Z= 0.285 Chirality : 0.050 0.473 536 Planarity : 0.005 0.039 612 Dihedral : 4.375 18.112 617 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.20 % Allowed : 7.16 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.42), residues: 427 helix: -3.90 (0.61), residues: 33 sheet: 0.31 (0.41), residues: 157 loop : 0.26 (0.43), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 67 TYR 0.017 0.002 TYR A 495 PHE 0.010 0.001 PHE A 429 TRP 0.012 0.001 TRP H 47 HIS 0.005 0.002 HIS L 92 Details of bonding type rmsd covalent geometry : bond 0.00537 ( 3534) covalent geometry : angle 0.53984 ( 4804) SS BOND : bond 0.00394 ( 6) SS BOND : angle 0.75013 ( 12) hydrogen bonds : bond 0.03569 ( 113) hydrogen bonds : angle 6.53211 ( 261) link_ALPHA1-3 : bond 0.01193 ( 1) link_ALPHA1-3 : angle 1.05080 ( 3) link_ALPHA1-6 : bond 0.00875 ( 1) link_ALPHA1-6 : angle 1.25401 ( 3) link_BETA1-4 : bond 0.00598 ( 2) link_BETA1-4 : angle 1.84884 ( 6) link_BETA1-6 : bond 0.00179 ( 1) link_BETA1-6 : angle 1.27390 ( 3) link_NAG-ASN : bond 0.01208 ( 2) link_NAG-ASN : angle 4.23654 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.104 Fit side-chains REVERT: A 378 LYS cc_start: 0.8815 (mttt) cc_final: 0.8045 (mtmt) REVERT: A 471 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8190 (mt-10) REVERT: H 43 GLN cc_start: 0.8502 (mm110) cc_final: 0.8160 (mp10) REVERT: H 70 MET cc_start: 0.9343 (mtt) cc_final: 0.8684 (mtt) REVERT: L 82 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8000 (pm20) outliers start: 8 outliers final: 7 residues processed: 34 average time/residue: 0.0346 time to fit residues: 1.7182 Evaluate side-chains 36 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 82 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 18 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 0 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3132 r_free = 0.3132 target = 0.112018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.096237 restraints weight = 4134.872| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 1.47 r_work: 0.2810 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3547 Z= 0.181 Angle : 0.603 15.490 4837 Z= 0.283 Chirality : 0.046 0.213 536 Planarity : 0.004 0.037 612 Dihedral : 4.914 47.367 617 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.20 % Allowed : 7.71 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.42), residues: 427 helix: -3.88 (0.61), residues: 33 sheet: 0.28 (0.41), residues: 157 loop : 0.20 (0.43), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 67 TYR 0.014 0.001 TYR A 495 PHE 0.008 0.001 PHE L 84 TRP 0.011 0.001 TRP H 47 HIS 0.004 0.002 HIS L 92 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 3534) covalent geometry : angle 0.51634 ( 4804) SS BOND : bond 0.00354 ( 6) SS BOND : angle 0.70987 ( 12) hydrogen bonds : bond 0.03425 ( 113) hydrogen bonds : angle 6.47363 ( 261) link_ALPHA1-3 : bond 0.01127 ( 1) link_ALPHA1-3 : angle 1.15342 ( 3) link_ALPHA1-6 : bond 0.00476 ( 1) link_ALPHA1-6 : angle 1.32376 ( 3) link_BETA1-4 : bond 0.00549 ( 2) link_BETA1-4 : angle 1.69684 ( 6) link_BETA1-6 : bond 0.00209 ( 1) link_BETA1-6 : angle 1.26878 ( 3) link_NAG-ASN : bond 0.02196 ( 2) link_NAG-ASN : angle 8.58735 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.133 Fit side-chains REVERT: A 378 LYS cc_start: 0.8816 (mttt) cc_final: 0.8067 (mtmt) REVERT: A 471 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8222 (mt-10) REVERT: H 43 GLN cc_start: 0.8507 (mm110) cc_final: 0.8234 (mp10) REVERT: H 70 MET cc_start: 0.9322 (mtt) cc_final: 0.8681 (mtt) REVERT: L 82 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8015 (pm20) outliers start: 8 outliers final: 7 residues processed: 36 average time/residue: 0.0345 time to fit residues: 1.8091 Evaluate side-chains 38 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 82 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 0.0060 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 0.0270 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 32 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 overall best weight: 0.3854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.139985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.120963 restraints weight = 3910.721| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 1.80 r_work: 0.2788 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3547 Z= 0.137 Angle : 0.559 13.798 4837 Z= 0.262 Chirality : 0.044 0.147 536 Planarity : 0.004 0.035 612 Dihedral : 4.728 40.282 617 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.65 % Allowed : 8.26 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.42), residues: 427 helix: -3.84 (0.62), residues: 33 sheet: 0.35 (0.42), residues: 157 loop : 0.29 (0.44), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 38 TYR 0.012 0.001 TYR A 369 PHE 0.007 0.001 PHE H 29 TRP 0.010 0.001 TRP H 47 HIS 0.004 0.001 HIS L 92 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 3534) covalent geometry : angle 0.48565 ( 4804) SS BOND : bond 0.00300 ( 6) SS BOND : angle 0.60980 ( 12) hydrogen bonds : bond 0.03192 ( 113) hydrogen bonds : angle 6.29600 ( 261) link_ALPHA1-3 : bond 0.00996 ( 1) link_ALPHA1-3 : angle 1.15716 ( 3) link_ALPHA1-6 : bond 0.00450 ( 1) link_ALPHA1-6 : angle 1.36837 ( 3) link_BETA1-4 : bond 0.00526 ( 2) link_BETA1-4 : angle 1.59231 ( 6) link_BETA1-6 : bond 0.00197 ( 1) link_BETA1-6 : angle 1.21516 ( 3) link_NAG-ASN : bond 0.01517 ( 2) link_NAG-ASN : angle 7.56900 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.122 Fit side-chains REVERT: A 378 LYS cc_start: 0.8757 (mttt) cc_final: 0.7973 (mtmt) REVERT: A 471 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8268 (mt-10) REVERT: H 43 GLN cc_start: 0.8451 (mm110) cc_final: 0.8186 (mp10) REVERT: H 70 MET cc_start: 0.9318 (mtt) cc_final: 0.9055 (mtt) REVERT: L 82 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8017 (pm20) outliers start: 6 outliers final: 4 residues processed: 34 average time/residue: 0.0444 time to fit residues: 2.1313 Evaluate side-chains 33 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 82 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 10 optimal weight: 0.2980 chunk 41 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 36 optimal weight: 0.3980 chunk 6 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3493 r_free = 0.3493 target = 0.138340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.119616 restraints weight = 3895.584| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 1.76 r_work: 0.2777 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 3547 Z= 0.176 Angle : 0.602 15.206 4837 Z= 0.282 Chirality : 0.046 0.286 536 Planarity : 0.004 0.037 612 Dihedral : 4.583 32.525 617 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.65 % Allowed : 7.71 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.43), residues: 427 helix: -3.49 (0.77), residues: 27 sheet: 0.32 (0.42), residues: 157 loop : 0.35 (0.44), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 67 TYR 0.013 0.001 TYR A 495 PHE 0.008 0.001 PHE L 84 TRP 0.011 0.001 TRP H 47 HIS 0.005 0.002 HIS L 92 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 3534) covalent geometry : angle 0.51887 ( 4804) SS BOND : bond 0.00347 ( 6) SS BOND : angle 0.68713 ( 12) hydrogen bonds : bond 0.03371 ( 113) hydrogen bonds : angle 6.37316 ( 261) link_ALPHA1-3 : bond 0.00955 ( 1) link_ALPHA1-3 : angle 1.21298 ( 3) link_ALPHA1-6 : bond 0.00431 ( 1) link_ALPHA1-6 : angle 1.35856 ( 3) link_BETA1-4 : bond 0.00505 ( 2) link_BETA1-4 : angle 1.66100 ( 6) link_BETA1-6 : bond 0.00188 ( 1) link_BETA1-6 : angle 1.17510 ( 3) link_NAG-ASN : bond 0.02330 ( 2) link_NAG-ASN : angle 8.38972 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.078 Fit side-chains REVERT: A 378 LYS cc_start: 0.8752 (mttt) cc_final: 0.7973 (mtmt) REVERT: A 471 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8274 (mt-10) REVERT: H 43 GLN cc_start: 0.8460 (mm110) cc_final: 0.8189 (mp10) REVERT: H 70 MET cc_start: 0.9323 (mtt) cc_final: 0.8653 (mtt) REVERT: L 82 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.7999 (pm20) outliers start: 6 outliers final: 5 residues processed: 32 average time/residue: 0.0385 time to fit residues: 1.7900 Evaluate side-chains 34 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 82 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 1 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.0870 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.0060 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 32 optimal weight: 0.5980 overall best weight: 0.2774 ------------------------------------------------------------------------------- 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 = 0.3522 r_free = 0.3522 target = 0.140738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.121940 restraints weight = 3873.659| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.78 r_work: 0.2811 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3547 Z= 0.118 Angle : 0.550 14.475 4837 Z= 0.255 Chirality : 0.044 0.216 536 Planarity : 0.004 0.034 612 Dihedral : 4.563 36.348 617 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.38 % Allowed : 8.26 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.43), residues: 427 helix: -3.50 (0.74), residues: 27 sheet: 0.59 (0.44), residues: 148 loop : 0.43 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 67 TYR 0.011 0.001 TYR A 369 PHE 0.007 0.001 PHE H 29 TRP 0.008 0.001 TRP H 47 HIS 0.003 0.001 HIS L 92 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 3534) covalent geometry : angle 0.46925 ( 4804) SS BOND : bond 0.00252 ( 6) SS BOND : angle 0.60492 ( 12) hydrogen bonds : bond 0.02994 ( 113) hydrogen bonds : angle 6.12030 ( 261) link_ALPHA1-3 : bond 0.00914 ( 1) link_ALPHA1-3 : angle 1.21966 ( 3) link_ALPHA1-6 : bond 0.00466 ( 1) link_ALPHA1-6 : angle 1.35977 ( 3) link_BETA1-4 : bond 0.00490 ( 2) link_BETA1-4 : angle 1.50841 ( 6) link_BETA1-6 : bond 0.00255 ( 1) link_BETA1-6 : angle 1.17351 ( 3) link_NAG-ASN : bond 0.02192 ( 2) link_NAG-ASN : angle 7.86603 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.079 Fit side-chains REVERT: A 378 LYS cc_start: 0.8719 (mttt) cc_final: 0.7934 (mtmt) REVERT: A 471 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8255 (mt-10) REVERT: H 70 MET cc_start: 0.9298 (mtt) cc_final: 0.8672 (mtt) REVERT: L 82 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8054 (pm20) outliers start: 5 outliers final: 4 residues processed: 35 average time/residue: 0.0617 time to fit residues: 2.8733 Evaluate side-chains 33 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 82 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.9214 > 50: distance: 76 - 99: 20.617 distance: 79 - 86: 13.788 distance: 80 - 107: 26.722 distance: 86 - 87: 11.614 distance: 87 - 88: 30.460 distance: 87 - 90: 10.026 distance: 88 - 89: 21.616 distance: 88 - 94: 11.927 distance: 89 - 119: 47.060 distance: 90 - 91: 8.438 distance: 90 - 92: 24.715 distance: 94 - 95: 18.513 distance: 95 - 96: 38.792 distance: 95 - 98: 30.588 distance: 96 - 97: 19.050 distance: 96 - 99: 39.515 distance: 99 - 100: 5.623 distance: 100 - 101: 18.323 distance: 100 - 103: 18.661 distance: 101 - 102: 20.761 distance: 101 - 107: 28.044 distance: 103 - 104: 10.791 distance: 104 - 105: 17.929 distance: 104 - 106: 17.890 distance: 107 - 108: 11.113 distance: 108 - 109: 11.461 distance: 108 - 111: 15.956 distance: 109 - 110: 42.410 distance: 109 - 119: 20.718 distance: 112 - 113: 16.423 distance: 112 - 114: 9.285 distance: 113 - 115: 6.286 distance: 114 - 116: 15.288 distance: 115 - 117: 7.130 distance: 116 - 117: 8.305 distance: 117 - 118: 11.398 distance: 119 - 120: 14.651 distance: 120 - 121: 10.430 distance: 120 - 123: 12.887 distance: 121 - 122: 6.166 distance: 121 - 127: 15.485 distance: 123 - 124: 3.875 distance: 124 - 126: 24.163 distance: 127 - 128: 16.448 distance: 128 - 129: 20.852 distance: 128 - 131: 21.311 distance: 129 - 130: 18.877 distance: 129 - 139: 15.407 distance: 131 - 132: 5.386 distance: 132 - 133: 8.833 distance: 132 - 134: 38.420 distance: 133 - 135: 23.460 distance: 134 - 136: 32.279 distance: 135 - 137: 39.895 distance: 136 - 137: 11.897 distance: 137 - 138: 4.962 distance: 139 - 140: 7.818 distance: 140 - 141: 40.406 distance: 141 - 142: 8.902 distance: 141 - 148: 36.559 distance: 143 - 144: 19.453 distance: 144 - 145: 41.919 distance: 145 - 146: 36.581 distance: 146 - 147: 40.192 distance: 148 - 149: 18.590 distance: 149 - 150: 8.916 distance: 149 - 152: 34.063 distance: 150 - 151: 19.505 distance: 150 - 156: 17.487 distance: 152 - 153: 19.239 distance: 153 - 154: 19.870 distance: 153 - 155: 34.408 distance: 156 - 157: 17.274 distance: 156 - 162: 19.698 distance: 157 - 158: 12.051 distance: 157 - 160: 15.094 distance: 158 - 159: 14.765 distance: 158 - 163: 10.062 distance: 160 - 161: 16.739 distance: 161 - 162: 13.414 distance: 163 - 164: 5.696 distance: 164 - 165: 6.938 distance: 164 - 167: 5.703 distance: 165 - 166: 17.731 distance: 165 - 171: 12.069 distance: 167 - 168: 8.624 distance: 168 - 169: 8.670 distance: 168 - 170: 10.977