Starting phenix.real_space_refine on Tue Mar 3 11:23:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e23_30950/03_2026/7e23_30950.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e23_30950/03_2026/7e23_30950.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/7e23_30950/03_2026/7e23_30950.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e23_30950/03_2026/7e23_30950.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e23_30950/03_2026/7e23_30950.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e23_30950/03_2026/7e23_30950.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= 0.001 sd= 0.053 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 13 5.16 5 C 2001 2.51 5 N 519 2.21 5 O 600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3133 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "B" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 756 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 94} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 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: 0.90, per 1000 atoms: 0.29 Number of scatterers: 3133 At special positions: 0 Unit cell: (60.48, 74.52, 99.36, 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 13 16.00 O 600 8.00 N 519 7.00 C 2001 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 343 " Time building additional restraints: 0.23 Conformation dependent library (CDL) restraints added in 118.3 milliseconds 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 736 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 8 sheets defined 4.7% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.628A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.614A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.574A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'B' and resid 19 through 22 Processing sheet with id=AA5, first strand: chain 'B' and resid 57 through 58 removed outlier: 3.541A pdb=" N ASN B 58 " --> pdb=" O GLU B 50 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU B 46 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N GLU B 50 " --> pdb=" O TRP B 34 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TRP B 34 " --> pdb=" O GLU B 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 91 through 92 removed outlier: 3.528A pdb=" N ALA B 91 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 19 through 23 removed outlier: 3.951A pdb=" N LEU C 73 " --> pdb=" O CYS C 23 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.593A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) 61 hydrogen bonds defined for protein. 141 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: 0.37 Time building geometry restraints manager: 0.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 985 1.34 - 1.46: 836 1.46 - 1.58: 1379 1.58 - 1.70: 0 1.70 - 1.82: 14 Bond restraints: 3214 Sorted by residual: bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.12e+00 bond pdb=" CB ARG B 66 " pdb=" CG ARG B 66 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.64e+00 bond pdb=" C SER B 70 " pdb=" N VAL B 71 " ideal model delta sigma weight residual 1.334 1.316 0.017 1.24e-02 6.50e+03 1.92e+00 bond pdb=" C5 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.413 1.437 -0.024 2.00e-02 2.50e+03 1.39e+00 bond pdb=" CD ARG B 66 " pdb=" NE ARG B 66 " ideal model delta sigma weight residual 1.458 1.442 0.016 1.40e-02 5.10e+03 1.27e+00 ... (remaining 3209 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 4236 2.00 - 4.00: 120 4.00 - 6.00: 12 6.00 - 8.01: 6 8.01 - 10.01: 3 Bond angle restraints: 4377 Sorted by residual: angle pdb=" N ARG C 61 " pdb=" CA ARG C 61 " pdb=" C ARG C 61 " ideal model delta sigma weight residual 114.75 108.44 6.31 1.26e+00 6.30e-01 2.51e+01 angle pdb=" CG ARG B 66 " pdb=" CD ARG B 66 " pdb=" NE ARG B 66 " ideal model delta sigma weight residual 112.00 101.99 10.01 2.20e+00 2.07e-01 2.07e+01 angle pdb=" C SER C 92 " pdb=" N ASN C 93 " pdb=" CA ASN C 93 " ideal model delta sigma weight residual 121.54 129.87 -8.33 1.91e+00 2.74e-01 1.90e+01 angle pdb=" C GLY C 68 " pdb=" N THR C 69 " pdb=" CA THR C 69 " ideal model delta sigma weight residual 121.54 128.28 -6.74 1.91e+00 2.74e-01 1.25e+01 angle pdb=" C ASN C 93 " pdb=" N TRP C 94 " pdb=" CA TRP C 94 " ideal model delta sigma weight residual 121.80 113.47 8.33 2.44e+00 1.68e-01 1.17e+01 ... (remaining 4372 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 1699 17.73 - 35.46: 159 35.46 - 53.19: 27 53.19 - 70.92: 5 70.92 - 88.64: 4 Dihedral angle restraints: 1894 sinusoidal: 733 harmonic: 1161 Sorted by residual: dihedral pdb=" CA PHE C 71 " pdb=" C PHE C 71 " pdb=" N THR C 72 " pdb=" CA THR C 72 " ideal model delta harmonic sigma weight residual 180.00 137.99 42.01 0 5.00e+00 4.00e-02 7.06e+01 dihedral pdb=" CA SER C 7 " pdb=" C SER C 7 " pdb=" N PRO C 8 " pdb=" CA PRO C 8 " ideal model delta harmonic sigma weight residual 180.00 -157.15 -22.85 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA THR C 69 " pdb=" C THR C 69 " pdb=" N ASP C 70 " pdb=" CA ASP C 70 " ideal model delta harmonic sigma weight residual 180.00 157.31 22.69 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 1891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 301 0.039 - 0.078: 124 0.078 - 0.117: 35 0.117 - 0.156: 16 0.156 - 0.195: 3 Chirality restraints: 479 Sorted by residual: chirality pdb=" CA PHE C 71 " pdb=" N PHE C 71 " pdb=" C PHE C 71 " pdb=" CB PHE C 71 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.46e-01 chirality pdb=" CB ILE C 58 " pdb=" CA ILE C 58 " pdb=" CG1 ILE C 58 " pdb=" CG2 ILE C 58 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.13e-01 chirality pdb=" CA ILE A 434 " pdb=" N ILE A 434 " pdb=" C ILE A 434 " pdb=" CB ILE A 434 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.73e-01 ... (remaining 476 not shown) Planarity restraints: 562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 60 " 0.039 5.00e-02 4.00e+02 5.88e-02 5.53e+00 pdb=" N PRO B 61 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 61 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 61 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 71 " -0.022 2.00e-02 2.50e+03 1.62e-02 4.61e+00 pdb=" CG PHE C 71 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE C 71 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE C 71 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 71 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 71 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 71 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 47 " 0.008 2.00e-02 2.50e+03 1.22e-02 3.74e+00 pdb=" CG TRP B 47 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP B 47 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP B 47 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 47 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 47 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 47 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 47 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 47 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 47 " 0.002 2.00e-02 2.50e+03 ... (remaining 559 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 82 2.68 - 3.23: 2966 3.23 - 3.79: 4598 3.79 - 4.34: 6234 4.34 - 4.90: 10604 Nonbonded interactions: 24484 Sorted by model distance: nonbonded pdb=" OH TYR C 36 " pdb=" OE1 GLN C 89 " model vdw 2.123 3.040 nonbonded pdb=" O SER C 63 " pdb=" OG SER C 77 " model vdw 2.215 3.040 nonbonded pdb=" OG SER C 7 " pdb=" OG SER C 22 " model vdw 2.220 3.040 nonbonded pdb=" O LYS A 417 " pdb=" ND2 ASN A 422 " model vdw 2.239 3.120 nonbonded pdb=" OG SER B 28 " pdb=" O HIS B 53 " model vdw 2.246 3.040 ... (remaining 24479 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.120 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.000 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3220 Z= 0.196 Angle : 0.827 10.007 4390 Z= 0.456 Chirality : 0.051 0.195 479 Planarity : 0.006 0.059 561 Dihedral : 14.521 88.644 1143 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.30 % Favored : 82.70 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -3.70 (0.41), residues: 393 helix: -5.03 (0.42), residues: 20 sheet: -2.14 (0.45), residues: 125 loop : -2.50 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 54 TYR 0.017 0.002 TYR C 49 PHE 0.036 0.002 PHE C 71 TRP 0.031 0.002 TRP B 47 HIS 0.000 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 3214) covalent geometry : angle 0.82520 ( 4377) SS BOND : bond 0.00134 ( 5) SS BOND : angle 1.22991 ( 10) hydrogen bonds : bond 0.17827 ( 61) hydrogen bonds : angle 8.42416 ( 141) link_NAG-ASN : bond 0.00091 ( 1) link_NAG-ASN : angle 1.20822 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.119 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0722 time to fit residues: 5.0181 Evaluate side-chains 46 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.3980 chunk 26 optimal weight: 0.0970 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 0.0370 chunk 37 optimal weight: 0.9990 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.151267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.138463 restraints weight = 4734.536| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.67 r_work: 0.3715 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3220 Z= 0.139 Angle : 0.729 8.495 4390 Z= 0.371 Chirality : 0.048 0.193 479 Planarity : 0.007 0.114 561 Dihedral : 7.003 41.730 463 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.27 % Favored : 84.73 % Rotamer: Outliers : 1.48 % Allowed : 11.83 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -3.60 (0.41), residues: 393 helix: -5.01 (0.43), residues: 20 sheet: -1.79 (0.45), residues: 126 loop : -2.60 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 66 TYR 0.013 0.001 TYR C 49 PHE 0.030 0.001 PHE C 71 TRP 0.012 0.001 TRP A 436 HIS 0.000 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 3214) covalent geometry : angle 0.72721 ( 4377) SS BOND : bond 0.00257 ( 5) SS BOND : angle 1.22848 ( 10) hydrogen bonds : bond 0.03638 ( 61) hydrogen bonds : angle 6.88143 ( 141) link_NAG-ASN : bond 0.00236 ( 1) link_NAG-ASN : angle 1.34726 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.106 Fit side-chains REVERT: A 516 GLU cc_start: 0.8244 (pt0) cc_final: 0.8041 (pt0) REVERT: C 36 TYR cc_start: 0.7364 (m-80) cc_final: 0.6634 (m-80) outliers start: 5 outliers final: 5 residues processed: 51 average time/residue: 0.0696 time to fit residues: 4.2942 Evaluate side-chains 48 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 47 TRP Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain C residue 53 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 7 optimal weight: 0.0570 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 23 optimal weight: 0.1980 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- 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 = 0.3958 r_free = 0.3958 target = 0.152216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.139542 restraints weight = 4705.978| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 1.62 r_work: 0.3728 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3220 Z= 0.133 Angle : 0.702 8.637 4390 Z= 0.355 Chirality : 0.047 0.185 479 Planarity : 0.006 0.100 561 Dihedral : 6.482 40.687 463 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.27 % Favored : 84.73 % Rotamer: Outliers : 2.66 % Allowed : 13.91 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -3.55 (0.41), residues: 393 helix: -4.87 (0.42), residues: 26 sheet: -1.70 (0.45), residues: 126 loop : -2.53 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 66 TYR 0.014 0.001 TYR C 49 PHE 0.029 0.001 PHE C 71 TRP 0.010 0.001 TRP A 436 HIS 0.000 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 3214) covalent geometry : angle 0.70009 ( 4377) SS BOND : bond 0.00212 ( 5) SS BOND : angle 1.03859 ( 10) hydrogen bonds : bond 0.03341 ( 61) hydrogen bonds : angle 6.53045 ( 141) link_NAG-ASN : bond 0.00189 ( 1) link_NAG-ASN : angle 1.43260 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.109 Fit side-chains REVERT: C 36 TYR cc_start: 0.7417 (m-80) cc_final: 0.6396 (m-80) outliers start: 9 outliers final: 9 residues processed: 55 average time/residue: 0.0704 time to fit residues: 4.6258 Evaluate side-chains 52 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 47 TRP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain C residue 96 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 1 optimal weight: 0.9980 chunk 35 optimal weight: 0.0870 chunk 24 optimal weight: 0.0670 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 0.1980 chunk 2 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.3696 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.153862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.140571 restraints weight = 4683.036| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 1.75 r_work: 0.3730 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3220 Z= 0.126 Angle : 0.684 9.507 4390 Z= 0.345 Chirality : 0.046 0.187 479 Planarity : 0.006 0.092 561 Dihedral : 6.188 39.317 463 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.50 % Favored : 85.50 % Rotamer: Outliers : 3.25 % Allowed : 15.98 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -3.45 (0.41), residues: 393 helix: -4.82 (0.46), residues: 26 sheet: -1.58 (0.46), residues: 126 loop : -2.48 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 66 TYR 0.012 0.001 TYR C 49 PHE 0.028 0.001 PHE C 71 TRP 0.010 0.001 TRP A 436 HIS 0.000 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 3214) covalent geometry : angle 0.68305 ( 4377) SS BOND : bond 0.00385 ( 5) SS BOND : angle 0.87932 ( 10) hydrogen bonds : bond 0.03126 ( 61) hydrogen bonds : angle 6.43417 ( 141) link_NAG-ASN : bond 0.00232 ( 1) link_NAG-ASN : angle 1.30280 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.113 Fit side-chains REVERT: A 454 ARG cc_start: 0.8793 (ttm-80) cc_final: 0.8571 (ttm-80) REVERT: C 36 TYR cc_start: 0.7463 (m-80) cc_final: 0.6476 (m-80) outliers start: 11 outliers final: 10 residues processed: 56 average time/residue: 0.0686 time to fit residues: 4.6138 Evaluate side-chains 57 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 47 TRP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 96 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.0970 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.3951 r_free = 0.3951 target = 0.151869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.138748 restraints weight = 4680.391| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 1.73 r_work: 0.3708 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3589 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3220 Z= 0.146 Angle : 0.709 13.308 4390 Z= 0.352 Chirality : 0.047 0.192 479 Planarity : 0.006 0.094 561 Dihedral : 6.239 38.563 463 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.52 % Favored : 84.48 % Rotamer: Outliers : 3.85 % Allowed : 17.75 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -3.40 (0.42), residues: 393 helix: -4.84 (0.46), residues: 26 sheet: -1.56 (0.46), residues: 126 loop : -2.44 (0.41), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 66 TYR 0.013 0.001 TYR C 49 PHE 0.032 0.002 PHE C 71 TRP 0.009 0.001 TRP A 436 HIS 0.001 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 3214) covalent geometry : angle 0.70567 ( 4377) SS BOND : bond 0.00214 ( 5) SS BOND : angle 1.42269 ( 10) hydrogen bonds : bond 0.03212 ( 61) hydrogen bonds : angle 6.33581 ( 141) link_NAG-ASN : bond 0.00177 ( 1) link_NAG-ASN : angle 1.44859 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.114 Fit side-chains REVERT: A 516 GLU cc_start: 0.8143 (pt0) cc_final: 0.7933 (pt0) REVERT: B 48 ILE cc_start: 0.8494 (pt) cc_final: 0.8278 (pt) REVERT: C 5 THR cc_start: 0.8314 (m) cc_final: 0.7798 (p) REVERT: C 36 TYR cc_start: 0.7520 (m-80) cc_final: 0.6642 (m-80) outliers start: 13 outliers final: 10 residues processed: 63 average time/residue: 0.0672 time to fit residues: 5.1132 Evaluate side-chains 62 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain C residue 96 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 14 optimal weight: 0.0870 chunk 28 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 = 0.3941 r_free = 0.3941 target = 0.151065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.138137 restraints weight = 4641.048| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 1.72 r_work: 0.3700 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3584 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3220 Z= 0.152 Angle : 0.701 10.794 4390 Z= 0.353 Chirality : 0.047 0.194 479 Planarity : 0.006 0.094 561 Dihedral : 6.241 38.585 463 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.03 % Favored : 83.97 % Rotamer: Outliers : 3.55 % Allowed : 18.93 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -3.37 (0.42), residues: 393 helix: -4.88 (0.42), residues: 26 sheet: -1.46 (0.46), residues: 126 loop : -2.45 (0.41), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 66 TYR 0.015 0.001 TYR B 59 PHE 0.034 0.002 PHE C 71 TRP 0.010 0.001 TRP A 436 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 3214) covalent geometry : angle 0.69774 ( 4377) SS BOND : bond 0.00330 ( 5) SS BOND : angle 1.31542 ( 10) hydrogen bonds : bond 0.03251 ( 61) hydrogen bonds : angle 6.26359 ( 141) link_NAG-ASN : bond 0.00188 ( 1) link_NAG-ASN : angle 1.43902 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.106 Fit side-chains REVERT: B 39 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7878 (tt0) REVERT: B 48 ILE cc_start: 0.8539 (pt) cc_final: 0.8324 (pt) REVERT: C 5 THR cc_start: 0.8295 (m) cc_final: 0.7768 (p) REVERT: C 36 TYR cc_start: 0.7524 (m-80) cc_final: 0.6658 (m-80) outliers start: 12 outliers final: 10 residues processed: 58 average time/residue: 0.0662 time to fit residues: 4.6541 Evaluate side-chains 56 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain C residue 96 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 8 optimal weight: 0.7980 chunk 24 optimal weight: 0.0770 chunk 12 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 chunk 31 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 18 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 = 0.3963 r_free = 0.3963 target = 0.153246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.140470 restraints weight = 4716.994| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 1.66 r_work: 0.3735 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3220 Z= 0.134 Angle : 0.717 11.792 4390 Z= 0.359 Chirality : 0.047 0.186 479 Planarity : 0.006 0.084 561 Dihedral : 6.071 37.429 463 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.50 % Favored : 85.50 % Rotamer: Outliers : 4.44 % Allowed : 20.41 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -3.32 (0.42), residues: 393 helix: -4.83 (0.46), residues: 26 sheet: -1.38 (0.46), residues: 126 loop : -2.45 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 66 TYR 0.013 0.001 TYR C 49 PHE 0.031 0.002 PHE C 71 TRP 0.011 0.001 TRP A 436 HIS 0.000 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 3214) covalent geometry : angle 0.71010 ( 4377) SS BOND : bond 0.00583 ( 5) SS BOND : angle 2.10019 ( 10) hydrogen bonds : bond 0.03113 ( 61) hydrogen bonds : angle 6.27407 ( 141) link_NAG-ASN : bond 0.00202 ( 1) link_NAG-ASN : angle 1.33719 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.115 Fit side-chains REVERT: A 516 GLU cc_start: 0.8050 (pt0) cc_final: 0.7828 (pt0) REVERT: B 48 ILE cc_start: 0.8560 (pt) cc_final: 0.8359 (pt) REVERT: C 5 THR cc_start: 0.8265 (m) cc_final: 0.7788 (p) REVERT: C 36 TYR cc_start: 0.7464 (m-80) cc_final: 0.6625 (m-80) outliers start: 15 outliers final: 10 residues processed: 60 average time/residue: 0.0580 time to fit residues: 4.3396 Evaluate side-chains 55 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain C residue 96 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 14 optimal weight: 0.0470 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 = 0.3821 r_free = 0.3821 target = 0.142304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.129239 restraints weight = 4820.032| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.92 r_work: 0.3582 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 3220 Z= 0.148 Angle : 0.733 11.734 4390 Z= 0.366 Chirality : 0.048 0.189 479 Planarity : 0.006 0.086 561 Dihedral : 6.154 37.624 463 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.52 % Favored : 84.48 % Rotamer: Outliers : 3.55 % Allowed : 21.60 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -3.21 (0.41), residues: 393 helix: -4.91 (0.42), residues: 26 sheet: -1.30 (0.49), residues: 116 loop : -2.34 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 66 TYR 0.012 0.001 TYR C 49 PHE 0.030 0.002 PHE C 71 TRP 0.010 0.002 TRP A 436 HIS 0.000 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 3214) covalent geometry : angle 0.72647 ( 4377) SS BOND : bond 0.00775 ( 5) SS BOND : angle 2.10885 ( 10) hydrogen bonds : bond 0.03261 ( 61) hydrogen bonds : angle 6.29916 ( 141) link_NAG-ASN : bond 0.00181 ( 1) link_NAG-ASN : angle 1.44225 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.103 Fit side-chains REVERT: A 516 GLU cc_start: 0.8247 (pt0) cc_final: 0.8005 (pt0) REVERT: B 39 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7808 (tt0) REVERT: C 5 THR cc_start: 0.8226 (m) cc_final: 0.7721 (p) REVERT: C 36 TYR cc_start: 0.7468 (m-80) cc_final: 0.6580 (m-80) outliers start: 12 outliers final: 11 residues processed: 58 average time/residue: 0.0661 time to fit residues: 4.6017 Evaluate side-chains 59 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3939 r_free = 0.3939 target = 0.151028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.137841 restraints weight = 4769.213| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 1.77 r_work: 0.3688 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 3220 Z= 0.173 Angle : 0.754 12.007 4390 Z= 0.379 Chirality : 0.049 0.197 479 Planarity : 0.006 0.090 561 Dihedral : 6.398 37.777 463 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.50 % Favored : 85.50 % Rotamer: Outliers : 4.44 % Allowed : 21.60 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -3.26 (0.41), residues: 393 helix: -5.01 (0.35), residues: 26 sheet: -1.36 (0.48), residues: 116 loop : -2.35 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 66 TYR 0.013 0.002 TYR C 49 PHE 0.038 0.002 PHE C 71 TRP 0.009 0.002 TRP B 112 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 3214) covalent geometry : angle 0.74740 ( 4377) SS BOND : bond 0.00724 ( 5) SS BOND : angle 2.12265 ( 10) hydrogen bonds : bond 0.03446 ( 61) hydrogen bonds : angle 6.30990 ( 141) link_NAG-ASN : bond 0.00150 ( 1) link_NAG-ASN : angle 1.50585 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.112 Fit side-chains REVERT: A 516 GLU cc_start: 0.8178 (pt0) cc_final: 0.7953 (pt0) REVERT: B 39 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7939 (tt0) REVERT: C 5 THR cc_start: 0.8239 (m) cc_final: 0.7706 (p) REVERT: C 36 TYR cc_start: 0.7548 (m-80) cc_final: 0.6653 (m-80) outliers start: 15 outliers final: 13 residues processed: 58 average time/residue: 0.0579 time to fit residues: 4.1601 Evaluate side-chains 63 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 19 optimal weight: 0.0870 chunk 2 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.3946 r_free = 0.3946 target = 0.151811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.138666 restraints weight = 4732.304| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 1.77 r_work: 0.3699 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3220 Z= 0.154 Angle : 0.740 12.426 4390 Z= 0.371 Chirality : 0.049 0.191 479 Planarity : 0.006 0.085 561 Dihedral : 6.329 38.707 463 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.54 % Favored : 83.46 % Rotamer: Outliers : 4.14 % Allowed : 22.19 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -3.22 (0.41), residues: 393 helix: -4.98 (0.36), residues: 26 sheet: -1.35 (0.48), residues: 116 loop : -2.32 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 66 TYR 0.013 0.001 TYR C 49 PHE 0.037 0.002 PHE C 71 TRP 0.011 0.002 TRP A 436 HIS 0.000 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 3214) covalent geometry : angle 0.73383 ( 4377) SS BOND : bond 0.00648 ( 5) SS BOND : angle 1.97849 ( 10) hydrogen bonds : bond 0.03479 ( 61) hydrogen bonds : angle 6.23632 ( 141) link_NAG-ASN : bond 0.00179 ( 1) link_NAG-ASN : angle 1.43155 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.112 Fit side-chains REVERT: A 516 GLU cc_start: 0.8180 (pt0) cc_final: 0.7947 (pt0) REVERT: B 39 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7886 (tt0) REVERT: C 5 THR cc_start: 0.8254 (m) cc_final: 0.7720 (p) REVERT: C 36 TYR cc_start: 0.7528 (m-80) cc_final: 0.6632 (m-80) outliers start: 14 outliers final: 13 residues processed: 57 average time/residue: 0.0659 time to fit residues: 4.5535 Evaluate side-chains 63 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 12 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.150291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.137072 restraints weight = 4810.347| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 1.78 r_work: 0.3680 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3220 Z= 0.174 Angle : 0.756 11.626 4390 Z= 0.380 Chirality : 0.049 0.196 479 Planarity : 0.006 0.092 561 Dihedral : 6.453 37.738 463 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.54 % Favored : 83.46 % Rotamer: Outliers : 4.44 % Allowed : 22.49 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -3.25 (0.41), residues: 393 helix: -4.98 (0.36), residues: 26 sheet: -1.39 (0.48), residues: 116 loop : -2.32 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 66 TYR 0.013 0.001 TYR C 49 PHE 0.040 0.002 PHE C 71 TRP 0.009 0.002 TRP A 436 HIS 0.001 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 3214) covalent geometry : angle 0.74961 ( 4377) SS BOND : bond 0.00653 ( 5) SS BOND : angle 2.00907 ( 10) hydrogen bonds : bond 0.03569 ( 61) hydrogen bonds : angle 6.34228 ( 141) link_NAG-ASN : bond 0.00162 ( 1) link_NAG-ASN : angle 1.45384 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 991.12 seconds wall clock time: 17 minutes 39.16 seconds (1059.16 seconds total)