Starting phenix.real_space_refine on Wed Jun 4 16:08:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wr9_32719/06_2025/7wr9_32719.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wr9_32719/06_2025/7wr9_32719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wr9_32719/06_2025/7wr9_32719.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wr9_32719/06_2025/7wr9_32719.map" model { file = "/net/cci-nas-00/data/ceres_data/7wr9_32719/06_2025/7wr9_32719.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wr9_32719/06_2025/7wr9_32719.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.032 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 15 5.16 5 C 2074 2.51 5 N 539 2.21 5 O 638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 3266 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 973 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 6, 'TRANS': 120} Chain: "B" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 780 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 9, 'TRANS': 94} Chain: "F" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1450 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 167} Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" 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: 3.18, per 1000 atoms: 0.97 Number of scatterers: 3266 At special positions: 0 Unit cell: (90.48, 63.44, 74.88, 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 15 16.00 O 638 8.00 N 539 7.00 C 2074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.02 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 87 " distance=2.03 Simple disulfide: pdb=" SG CYS F 323 " - pdb=" SG CYS F 348 " distance=2.03 Simple disulfide: pdb=" SG CYS F 366 " - pdb=" SG CYS F 419 " distance=2.03 Simple disulfide: pdb=" SG CYS F 467 " - pdb=" SG CYS F 474 " 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " BETA1-6 " NAG C 1 " - " FUC C 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG C 1 " - " ASN F 330 " " NAG F 601 " - " ASN F 357 " Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 392.8 milliseconds 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 748 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 8 sheets defined 3.9% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 87 through 91 removed outlier: 4.057A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 397 Processing helix chain 'F' and resid 425 through 430 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 removed outlier: 3.997A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 11 removed outlier: 3.518A pdb=" N ALA A 92 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE A 34 " --> pdb=" O LYS A 50 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LYS A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR A 59 " --> pdb=" O LYS A 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 18 through 20 Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 5 Processing sheet with id=AA5, first strand: chain 'B' and resid 9 through 10 removed outlier: 3.541A pdb=" N VAL B 10 " --> pdb=" O LYS B 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 44 through 47 removed outlier: 6.485A pdb=" N TRP B 34 " --> pdb=" O VAL B 46 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 341 through 345 removed outlier: 4.027A pdb=" N GLU F 341 " --> pdb=" O SER F 386 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN F 381 " --> pdb=" O GLU F 502 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 439 through 441 82 hydrogen bonds defined for protein. 207 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: 0.77 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 525 1.32 - 1.45: 1011 1.45 - 1.57: 1802 1.57 - 1.70: 0 1.70 - 1.82: 19 Bond restraints: 3357 Sorted by residual: bond pdb=" C PRO A 102 " pdb=" O PRO A 102 " ideal model delta sigma weight residual 1.235 1.196 0.039 1.30e-02 5.92e+03 9.14e+00 bond pdb=" CA TYR A 107 " pdb=" C TYR A 107 " ideal model delta sigma weight residual 1.529 1.498 0.031 1.04e-02 9.25e+03 9.05e+00 bond pdb=" N PRO A 102 " pdb=" CA PRO A 102 " ideal model delta sigma weight residual 1.469 1.432 0.036 1.28e-02 6.10e+03 8.02e+00 bond pdb=" N SER A 104 " pdb=" CA SER A 104 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.46e+00 bond pdb=" N ASP A 105 " pdb=" CA ASP A 105 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.41e-02 5.03e+03 6.45e+00 ... (remaining 3352 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 4507 3.66 - 7.31: 64 7.31 - 10.97: 6 10.97 - 14.62: 1 14.62 - 18.28: 1 Bond angle restraints: 4579 Sorted by residual: angle pdb=" N PRO A 106 " pdb=" CA PRO A 106 " pdb=" CB PRO A 106 " ideal model delta sigma weight residual 103.25 92.17 11.08 1.05e+00 9.07e-01 1.11e+02 angle pdb=" C PRO A 106 " pdb=" CA PRO A 106 " pdb=" CB PRO A 106 " ideal model delta sigma weight residual 111.56 120.78 -9.22 1.65e+00 3.67e-01 3.12e+01 angle pdb=" CA LEU B 27 " pdb=" CB LEU B 27 " pdb=" CG LEU B 27 " ideal model delta sigma weight residual 116.30 134.58 -18.28 3.50e+00 8.16e-02 2.73e+01 angle pdb=" C ASP B 91 " pdb=" N ALA B 92 " pdb=" CA ALA B 92 " ideal model delta sigma weight residual 121.54 130.69 -9.15 1.91e+00 2.74e-01 2.30e+01 angle pdb=" C TYR A 107 " pdb=" CA TYR A 107 " pdb=" CB TYR A 107 " ideal model delta sigma weight residual 111.43 105.49 5.94 1.24e+00 6.50e-01 2.29e+01 ... (remaining 4574 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.95: 1912 24.95 - 49.89: 95 49.89 - 74.83: 11 74.83 - 99.78: 10 99.78 - 124.72: 5 Dihedral angle restraints: 2033 sinusoidal: 847 harmonic: 1186 Sorted by residual: dihedral pdb=" CA LEU B 27 " pdb=" C LEU B 27 " pdb=" N PRO B 28 " pdb=" CA PRO B 28 " ideal model delta harmonic sigma weight residual 180.00 145.93 34.07 0 5.00e+00 4.00e-02 4.64e+01 dihedral pdb=" CB CYS F 467 " pdb=" SG CYS F 467 " pdb=" SG CYS F 474 " pdb=" CB CYS F 474 " ideal model delta sinusoidal sigma weight residual -86.00 -130.82 44.82 1 1.00e+01 1.00e-02 2.79e+01 dihedral pdb=" CA ALA B 92 " pdb=" C ALA B 92 " pdb=" N SER B 93 " pdb=" CA SER B 93 " ideal model delta harmonic sigma weight residual 180.00 154.30 25.70 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 2030 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 398 0.061 - 0.121: 86 0.121 - 0.181: 14 0.181 - 0.242: 4 0.242 - 0.302: 3 Chirality restraints: 505 Sorted by residual: chirality pdb=" CA ARG A 100 " pdb=" N ARG A 100 " pdb=" C ARG A 100 " pdb=" CB ARG A 100 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA TYR A 107 " pdb=" N TYR A 107 " pdb=" C TYR A 107 " pdb=" CB TYR A 107 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 502 not shown) Planarity restraints: 587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 109 " 0.017 2.00e-02 2.50e+03 2.81e-02 1.97e+01 pdb=" CG TRP A 109 " -0.072 2.00e-02 2.50e+03 pdb=" CD1 TRP A 109 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TRP A 109 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 109 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 109 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 109 " 0.021 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 109 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 109 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 109 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 105 " 0.018 2.00e-02 2.50e+03 3.61e-02 1.31e+01 pdb=" C ASP A 105 " -0.063 2.00e-02 2.50e+03 pdb=" O ASP A 105 " 0.023 2.00e-02 2.50e+03 pdb=" N PRO A 106 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 118 " 0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C VAL A 118 " -0.059 2.00e-02 2.50e+03 pdb=" O VAL A 118 " 0.023 2.00e-02 2.50e+03 pdb=" N TRP A 119 " 0.020 2.00e-02 2.50e+03 ... (remaining 584 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1152 2.86 - 3.37: 2584 3.37 - 3.88: 5412 3.88 - 4.39: 6083 4.39 - 4.90: 10951 Nonbonded interactions: 26182 Sorted by model distance: nonbonded pdb=" O VAL A 108 " pdb=" OG SER A 111 " model vdw 2.350 3.040 nonbonded pdb=" O ALA F 430 " pdb=" OG1 THR F 485 " model vdw 2.389 3.040 nonbonded pdb=" OG SER B 93 " pdb=" OG1 THR B 95 " model vdw 2.408 3.040 nonbonded pdb=" O GLY B 76 " pdb=" NE2 GLN B 78 " model vdw 2.413 3.120 nonbonded pdb=" O SER B 62 " pdb=" OG SER B 62 " model vdw 2.421 3.040 ... (remaining 26177 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: 3.280 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.500 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 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 : 0.006 0.043 3367 Z= 0.282 Angle : 1.055 18.280 4604 Z= 0.592 Chirality : 0.058 0.302 505 Planarity : 0.009 0.075 585 Dihedral : 17.104 124.722 1270 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.49 % Allowed : 9.63 % Favored : 89.88 % Rotamer: Outliers : 1.15 % Allowed : 0.86 % Favored : 97.99 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.39), residues: 405 helix: -4.46 (0.69), residues: 25 sheet: -1.38 (0.43), residues: 131 loop : -1.78 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.004 TRP A 109 HIS 0.002 0.001 HIS B 97 PHE 0.030 0.003 PHE F 364 TYR 0.040 0.002 TYR F 442 ARG 0.013 0.001 ARG A 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00121 ( 2) link_NAG-ASN : angle 1.65290 ( 6) link_BETA1-4 : bond 0.00863 ( 2) link_BETA1-4 : angle 1.85134 ( 6) hydrogen bonds : bond 0.26428 ( 82) hydrogen bonds : angle 9.68833 ( 207) link_BETA1-6 : bond 0.00513 ( 1) link_BETA1-6 : angle 1.12471 ( 3) SS BOND : bond 0.00362 ( 5) SS BOND : angle 1.29758 ( 10) covalent geometry : bond 0.00569 ( 3357) covalent geometry : angle 1.05147 ( 4579) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 80 GLU cc_start: 0.6819 (pm20) cc_final: 0.6519 (pt0) outliers start: 4 outliers final: 1 residues processed: 66 average time/residue: 0.1888 time to fit residues: 14.8347 Evaluate side-chains 55 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3644 r_free = 0.3644 target = 0.147266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.121706 restraints weight = 3860.678| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.19 r_work: 0.3188 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 3367 Z= 0.190 Angle : 0.699 9.675 4604 Z= 0.353 Chirality : 0.047 0.157 505 Planarity : 0.008 0.118 585 Dihedral : 13.162 110.376 561 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.37 % Favored : 89.38 % Rotamer: Outliers : 1.44 % Allowed : 9.48 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.41), residues: 405 helix: -4.74 (0.48), residues: 27 sheet: -1.24 (0.43), residues: 133 loop : -1.47 (0.40), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 109 HIS 0.005 0.001 HIS A 35 PHE 0.016 0.002 PHE F 334 TYR 0.014 0.001 TYR F 356 ARG 0.003 0.001 ARG B 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00084 ( 2) link_NAG-ASN : angle 1.22770 ( 6) link_BETA1-4 : bond 0.00905 ( 2) link_BETA1-4 : angle 2.22711 ( 6) hydrogen bonds : bond 0.04702 ( 82) hydrogen bonds : angle 7.01195 ( 207) link_BETA1-6 : bond 0.01016 ( 1) link_BETA1-6 : angle 1.91724 ( 3) SS BOND : bond 0.00674 ( 5) SS BOND : angle 1.00110 ( 10) covalent geometry : bond 0.00447 ( 3357) covalent geometry : angle 0.69164 ( 4579) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7342 (OUTLIER) cc_final: 0.7031 (p0) REVERT: B 78 GLN cc_start: 0.7446 (mp10) cc_final: 0.7220 (mp10) REVERT: F 407 ASP cc_start: 0.8508 (m-30) cc_final: 0.7979 (m-30) outliers start: 5 outliers final: 2 residues processed: 65 average time/residue: 0.1786 time to fit residues: 13.9062 Evaluate side-chains 61 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 44 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 3 optimal weight: 0.4980 chunk 36 optimal weight: 8.9990 chunk 37 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 0.0040 chunk 17 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- 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 = 0.3661 r_free = 0.3661 target = 0.148848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.123053 restraints weight = 3825.419| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.22 r_work: 0.3181 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 3367 Z= 0.155 Angle : 0.633 8.198 4604 Z= 0.317 Chirality : 0.046 0.144 505 Planarity : 0.007 0.117 585 Dihedral : 10.665 103.654 558 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.89 % Favored : 90.86 % Rotamer: Outliers : 2.87 % Allowed : 10.34 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.42), residues: 405 helix: -4.83 (0.39), residues: 27 sheet: -1.07 (0.45), residues: 133 loop : -1.29 (0.42), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 109 HIS 0.003 0.001 HIS A 35 PHE 0.016 0.001 PHE F 334 TYR 0.013 0.001 TYR F 356 ARG 0.002 0.000 ARG B 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00098 ( 2) link_NAG-ASN : angle 0.86048 ( 6) link_BETA1-4 : bond 0.00651 ( 2) link_BETA1-4 : angle 1.83756 ( 6) hydrogen bonds : bond 0.03667 ( 82) hydrogen bonds : angle 6.33609 ( 207) link_BETA1-6 : bond 0.00888 ( 1) link_BETA1-6 : angle 1.77081 ( 3) SS BOND : bond 0.00238 ( 5) SS BOND : angle 0.65693 ( 10) covalent geometry : bond 0.00379 ( 3357) covalent geometry : angle 0.62813 ( 4579) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 109 TRP cc_start: 0.7594 (OUTLIER) cc_final: 0.6832 (t60) REVERT: B 41 GLN cc_start: 0.7451 (pm20) cc_final: 0.7202 (pm20) REVERT: B 78 GLN cc_start: 0.7358 (mp10) cc_final: 0.7157 (mp10) outliers start: 10 outliers final: 8 residues processed: 71 average time/residue: 0.1790 time to fit residues: 15.3221 Evaluate side-chains 71 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 109 TRP Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 467 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 35 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 23 optimal weight: 0.0050 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 0.0170 chunk 10 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 34 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.3432 ------------------------------------------------------------------------------- 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 = 0.3669 r_free = 0.3669 target = 0.149322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.123647 restraints weight = 3902.380| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.23 r_work: 0.3230 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 3367 Z= 0.116 Angle : 0.586 7.546 4604 Z= 0.293 Chirality : 0.044 0.145 505 Planarity : 0.007 0.114 585 Dihedral : 9.504 99.981 558 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.90 % Favored : 91.85 % Rotamer: Outliers : 1.72 % Allowed : 15.80 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.43), residues: 405 helix: -4.80 (0.39), residues: 27 sheet: -0.90 (0.44), residues: 133 loop : -1.18 (0.44), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 109 HIS 0.001 0.000 HIS A 35 PHE 0.009 0.001 PHE A 101 TYR 0.012 0.001 TYR F 356 ARG 0.001 0.000 ARG A 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00181 ( 2) link_NAG-ASN : angle 0.71274 ( 6) link_BETA1-4 : bond 0.00602 ( 2) link_BETA1-4 : angle 1.64365 ( 6) hydrogen bonds : bond 0.02991 ( 82) hydrogen bonds : angle 6.01151 ( 207) link_BETA1-6 : bond 0.00996 ( 1) link_BETA1-6 : angle 1.89045 ( 3) SS BOND : bond 0.00208 ( 5) SS BOND : angle 0.60038 ( 10) covalent geometry : bond 0.00298 ( 3357) covalent geometry : angle 0.58086 ( 4579) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8717 (mtm180) cc_final: 0.8459 (mtm180) REVERT: A 109 TRP cc_start: 0.7440 (OUTLIER) cc_final: 0.6774 (t60) REVERT: B 41 GLN cc_start: 0.7404 (pm20) cc_final: 0.7158 (pm20) outliers start: 6 outliers final: 3 residues processed: 59 average time/residue: 0.1831 time to fit residues: 13.1780 Evaluate side-chains 60 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 TRP Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain F residue 385 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 32 optimal weight: 1.9990 chunk 4 optimal weight: 0.0770 chunk 0 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 = 0.3645 r_free = 0.3645 target = 0.147095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.121113 restraints weight = 3898.693| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.23 r_work: 0.3179 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 3367 Z= 0.156 Angle : 0.631 12.099 4604 Z= 0.308 Chirality : 0.044 0.150 505 Planarity : 0.007 0.115 585 Dihedral : 9.556 101.402 558 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.40 % Favored : 91.36 % Rotamer: Outliers : 2.30 % Allowed : 16.38 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.44), residues: 405 helix: -4.84 (0.36), residues: 27 sheet: -0.86 (0.44), residues: 133 loop : -1.06 (0.45), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 109 HIS 0.003 0.001 HIS A 35 PHE 0.011 0.001 PHE F 334 TYR 0.012 0.001 TYR F 356 ARG 0.002 0.000 ARG A 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00086 ( 2) link_NAG-ASN : angle 0.95956 ( 6) link_BETA1-4 : bond 0.00541 ( 2) link_BETA1-4 : angle 1.54862 ( 6) hydrogen bonds : bond 0.03137 ( 82) hydrogen bonds : angle 5.97233 ( 207) link_BETA1-6 : bond 0.00951 ( 1) link_BETA1-6 : angle 1.86727 ( 3) SS BOND : bond 0.00312 ( 5) SS BOND : angle 0.91205 ( 10) covalent geometry : bond 0.00388 ( 3357) covalent geometry : angle 0.62631 ( 4579) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 109 TRP cc_start: 0.7643 (OUTLIER) cc_final: 0.6828 (t60) outliers start: 8 outliers final: 7 residues processed: 67 average time/residue: 0.1729 time to fit residues: 13.9032 Evaluate side-chains 68 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 TRP Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 404 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 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 = 0.3625 r_free = 0.3625 target = 0.145281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.119232 restraints weight = 4012.373| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.25 r_work: 0.3157 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 3367 Z= 0.170 Angle : 0.632 9.191 4604 Z= 0.314 Chirality : 0.045 0.152 505 Planarity : 0.007 0.115 585 Dihedral : 9.655 101.778 558 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.40 % Favored : 91.36 % Rotamer: Outliers : 3.45 % Allowed : 16.09 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.44), residues: 405 helix: -4.87 (0.34), residues: 27 sheet: -0.83 (0.44), residues: 133 loop : -1.08 (0.44), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 109 HIS 0.004 0.001 HIS A 35 PHE 0.010 0.001 PHE F 334 TYR 0.013 0.001 TYR F 356 ARG 0.002 0.000 ARG A 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00129 ( 2) link_NAG-ASN : angle 0.97403 ( 6) link_BETA1-4 : bond 0.00532 ( 2) link_BETA1-4 : angle 1.51235 ( 6) hydrogen bonds : bond 0.03118 ( 82) hydrogen bonds : angle 5.95213 ( 207) link_BETA1-6 : bond 0.00892 ( 1) link_BETA1-6 : angle 1.79353 ( 3) SS BOND : bond 0.00331 ( 5) SS BOND : angle 0.90228 ( 10) covalent geometry : bond 0.00420 ( 3357) covalent geometry : angle 0.62715 ( 4579) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8741 (mtm180) cc_final: 0.8071 (mtm180) REVERT: A 109 TRP cc_start: 0.7945 (OUTLIER) cc_final: 0.6943 (t60) outliers start: 12 outliers final: 10 residues processed: 65 average time/residue: 0.1636 time to fit residues: 13.0042 Evaluate side-chains 70 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 109 TRP Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 467 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 36 optimal weight: 0.0040 chunk 5 optimal weight: 0.5980 chunk 0 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 7 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 = 0.3622 r_free = 0.3622 target = 0.146124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.119840 restraints weight = 3912.459| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.30 r_work: 0.3155 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 3367 Z= 0.133 Angle : 0.603 8.594 4604 Z= 0.299 Chirality : 0.044 0.152 505 Planarity : 0.007 0.114 585 Dihedral : 9.398 99.375 558 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.90 % Favored : 91.85 % Rotamer: Outliers : 2.30 % Allowed : 17.53 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.44), residues: 405 helix: -4.89 (0.32), residues: 27 sheet: -0.80 (0.44), residues: 133 loop : -1.02 (0.45), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 109 HIS 0.002 0.001 HIS A 35 PHE 0.009 0.001 PHE A 101 TYR 0.012 0.001 TYR F 356 ARG 0.002 0.000 ARG A 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00098 ( 2) link_NAG-ASN : angle 0.78430 ( 6) link_BETA1-4 : bond 0.00520 ( 2) link_BETA1-4 : angle 1.40747 ( 6) hydrogen bonds : bond 0.02906 ( 82) hydrogen bonds : angle 5.80918 ( 207) link_BETA1-6 : bond 0.01015 ( 1) link_BETA1-6 : angle 1.92668 ( 3) SS BOND : bond 0.00250 ( 5) SS BOND : angle 0.82217 ( 10) covalent geometry : bond 0.00335 ( 3357) covalent geometry : angle 0.59872 ( 4579) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.334 Fit side-chains REVERT: A 56 ARG cc_start: 0.8715 (mtm180) cc_final: 0.8024 (mtm180) REVERT: A 109 TRP cc_start: 0.7858 (OUTLIER) cc_final: 0.6910 (t60) REVERT: F 366 CYS cc_start: 0.7410 (m) cc_final: 0.7029 (m) outliers start: 8 outliers final: 7 residues processed: 60 average time/residue: 0.1692 time to fit residues: 12.3281 Evaluate side-chains 64 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 109 TRP Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 467 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3611 r_free = 0.3611 target = 0.145214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.118735 restraints weight = 3923.762| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.30 r_work: 0.3138 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 3367 Z= 0.161 Angle : 0.621 8.812 4604 Z= 0.309 Chirality : 0.044 0.154 505 Planarity : 0.007 0.114 585 Dihedral : 9.486 100.108 558 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.64 % Favored : 91.11 % Rotamer: Outliers : 3.16 % Allowed : 17.53 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.44), residues: 405 helix: -4.90 (0.31), residues: 27 sheet: -0.79 (0.44), residues: 133 loop : -1.00 (0.45), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 109 HIS 0.003 0.001 HIS A 35 PHE 0.009 0.001 PHE F 334 TYR 0.012 0.001 TYR F 356 ARG 0.002 0.000 ARG A 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00151 ( 2) link_NAG-ASN : angle 0.92800 ( 6) link_BETA1-4 : bond 0.00520 ( 2) link_BETA1-4 : angle 1.45293 ( 6) hydrogen bonds : bond 0.03009 ( 82) hydrogen bonds : angle 5.82430 ( 207) link_BETA1-6 : bond 0.00942 ( 1) link_BETA1-6 : angle 1.87911 ( 3) SS BOND : bond 0.00316 ( 5) SS BOND : angle 0.88249 ( 10) covalent geometry : bond 0.00400 ( 3357) covalent geometry : angle 0.61638 ( 4579) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.326 Fit side-chains REVERT: A 56 ARG cc_start: 0.8736 (mtm180) cc_final: 0.8038 (mtm180) REVERT: A 109 TRP cc_start: 0.8012 (OUTLIER) cc_final: 0.6910 (t60) REVERT: B 80 GLU cc_start: 0.7426 (pm20) cc_final: 0.7197 (pm20) REVERT: F 366 CYS cc_start: 0.7438 (m) cc_final: 0.7055 (m) outliers start: 11 outliers final: 9 residues processed: 62 average time/residue: 0.1736 time to fit residues: 13.0529 Evaluate side-chains 68 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 109 TRP Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 467 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 1 optimal weight: 0.7980 chunk 35 optimal weight: 0.2980 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 22 optimal weight: 0.0470 chunk 4 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 = 0.3627 r_free = 0.3627 target = 0.146620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.120352 restraints weight = 3940.515| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.28 r_work: 0.3179 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 3367 Z= 0.134 Angle : 0.599 8.712 4604 Z= 0.298 Chirality : 0.044 0.152 505 Planarity : 0.007 0.113 585 Dihedral : 9.273 98.027 558 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.41 % Favored : 92.35 % Rotamer: Outliers : 3.16 % Allowed : 17.82 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.44), residues: 405 helix: -4.88 (0.32), residues: 27 sheet: -0.75 (0.45), residues: 133 loop : -0.96 (0.45), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 109 HIS 0.002 0.001 HIS A 35 PHE 0.009 0.001 PHE A 101 TYR 0.012 0.001 TYR F 356 ARG 0.002 0.000 ARG A 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00108 ( 2) link_NAG-ASN : angle 0.75089 ( 6) link_BETA1-4 : bond 0.00523 ( 2) link_BETA1-4 : angle 1.36694 ( 6) hydrogen bonds : bond 0.02853 ( 82) hydrogen bonds : angle 5.71794 ( 207) link_BETA1-6 : bond 0.01007 ( 1) link_BETA1-6 : angle 1.97876 ( 3) SS BOND : bond 0.00233 ( 5) SS BOND : angle 0.81051 ( 10) covalent geometry : bond 0.00338 ( 3357) covalent geometry : angle 0.59511 ( 4579) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.327 Fit side-chains REVERT: A 56 ARG cc_start: 0.8704 (mtm180) cc_final: 0.8052 (mtm180) REVERT: A 109 TRP cc_start: 0.7967 (OUTLIER) cc_final: 0.7011 (t60) REVERT: F 366 CYS cc_start: 0.7402 (m) cc_final: 0.7015 (m) outliers start: 11 outliers final: 9 residues processed: 65 average time/residue: 0.1605 time to fit residues: 12.7515 Evaluate side-chains 69 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 109 TRP Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 467 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 29 optimal weight: 0.8980 chunk 17 optimal weight: 0.0030 chunk 37 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 23 optimal weight: 0.0980 chunk 34 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 overall best weight: 0.3390 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.148690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.123213 restraints weight = 3828.283| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.19 r_work: 0.3233 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 3367 Z= 0.116 Angle : 0.596 8.249 4604 Z= 0.295 Chirality : 0.044 0.153 505 Planarity : 0.007 0.112 585 Dihedral : 8.916 94.819 558 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.16 % Favored : 92.59 % Rotamer: Outliers : 2.59 % Allowed : 17.82 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.44), residues: 405 helix: -4.72 (0.42), residues: 20 sheet: -0.65 (0.45), residues: 133 loop : -1.02 (0.44), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 109 HIS 0.001 0.000 HIS A 35 PHE 0.009 0.001 PHE A 101 TYR 0.012 0.001 TYR F 356 ARG 0.003 0.000 ARG A 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00116 ( 2) link_NAG-ASN : angle 0.63412 ( 6) link_BETA1-4 : bond 0.00528 ( 2) link_BETA1-4 : angle 1.30455 ( 6) hydrogen bonds : bond 0.02759 ( 82) hydrogen bonds : angle 5.58648 ( 207) link_BETA1-6 : bond 0.01130 ( 1) link_BETA1-6 : angle 2.12369 ( 3) SS BOND : bond 0.00179 ( 5) SS BOND : angle 0.77489 ( 10) covalent geometry : bond 0.00300 ( 3357) covalent geometry : angle 0.59215 ( 4579) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8665 (mtm180) cc_final: 0.8033 (mtm180) REVERT: A 109 TRP cc_start: 0.7837 (OUTLIER) cc_final: 0.6983 (t60) REVERT: F 366 CYS cc_start: 0.7313 (m) cc_final: 0.6913 (m) outliers start: 9 outliers final: 8 residues processed: 62 average time/residue: 0.1658 time to fit residues: 12.4876 Evaluate side-chains 67 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 109 TRP Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 467 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 14 optimal weight: 0.4980 chunk 13 optimal weight: 0.0870 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 = 0.3661 r_free = 0.3661 target = 0.148389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.122557 restraints weight = 3926.630| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.24 r_work: 0.3219 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 3367 Z= 0.135 Angle : 0.603 8.336 4604 Z= 0.300 Chirality : 0.044 0.153 505 Planarity : 0.007 0.113 585 Dihedral : 8.984 94.929 558 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.65 % Favored : 92.10 % Rotamer: Outliers : 2.87 % Allowed : 17.53 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.44), residues: 405 helix: -4.73 (0.41), residues: 20 sheet: -0.70 (0.44), residues: 133 loop : -1.04 (0.44), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 109 HIS 0.002 0.001 HIS A 35 PHE 0.009 0.001 PHE A 101 TYR 0.012 0.001 TYR F 356 ARG 0.002 0.000 ARG A 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00112 ( 2) link_NAG-ASN : angle 0.75173 ( 6) link_BETA1-4 : bond 0.00521 ( 2) link_BETA1-4 : angle 1.34070 ( 6) hydrogen bonds : bond 0.02770 ( 82) hydrogen bonds : angle 5.66171 ( 207) link_BETA1-6 : bond 0.01042 ( 1) link_BETA1-6 : angle 2.10336 ( 3) SS BOND : bond 0.00260 ( 5) SS BOND : angle 1.02464 ( 10) covalent geometry : bond 0.00342 ( 3357) covalent geometry : angle 0.59776 ( 4579) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2322.04 seconds wall clock time: 40 minutes 40.61 seconds (2440.61 seconds total)