Starting phenix.real_space_refine on Wed Jul 23 11:02:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e23_30950/07_2025/7e23_30950.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e23_30950/07_2025/7e23_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7e23_30950/07_2025/7e23_30950.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e23_30950/07_2025/7e23_30950.map" model { file = "/net/cci-nas-00/data/ceres_data/7e23_30950/07_2025/7e23_30950.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e23_30950/07_2025/7e23_30950.cif" } resolution = 3.3 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= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 2.89, per 1000 atoms: 0.92 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: 0.66 Conformation dependent library (CDL) restraints added in 354.3 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: 0.36 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: 0.72 Time building geometry restraints manager: 0.82 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: 2.100 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.540 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.920 ------------------------------------------------------------------------------- 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 : 14.37 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 (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: -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 TRP 0.031 0.002 TRP B 47 HIS 0.000 0.000 HIS A 519 PHE 0.036 0.002 PHE C 71 TYR 0.017 0.002 TYR C 49 ARG 0.004 0.001 ARG C 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00091 ( 1) link_NAG-ASN : angle 1.20822 ( 3) hydrogen bonds : bond 0.17827 ( 61) hydrogen bonds : angle 8.42416 ( 141) SS BOND : bond 0.00134 ( 5) SS BOND : angle 1.22991 ( 10) covalent geometry : bond 0.00440 ( 3214) covalent geometry : angle 0.82520 ( 4377) *********************** 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 : 0.350 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1734 time to fit residues: 12.0846 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 : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 16 optimal weight: 0.0050 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 22 optimal weight: 0.0070 chunk 35 optimal weight: 3.9990 overall best weight: 0.4612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN B 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.150960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.138216 restraints weight = 4671.225| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 1.65 r_work: 0.3708 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3220 Z= 0.145 Angle : 0.734 8.153 4390 Z= 0.375 Chirality : 0.048 0.191 479 Planarity : 0.007 0.117 561 Dihedral : 7.026 41.899 463 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.52 % Favored : 84.48 % Rotamer: Outliers : 1.78 % Allowed : 11.54 % 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 (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: -3.61 (0.41), residues: 393 helix: -5.02 (0.42), residues: 20 sheet: -1.81 (0.45), residues: 126 loop : -2.60 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.000 0.000 HIS A 519 PHE 0.030 0.001 PHE C 71 TYR 0.013 0.001 TYR C 49 ARG 0.012 0.001 ARG B 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00239 ( 1) link_NAG-ASN : angle 1.36867 ( 3) hydrogen bonds : bond 0.03564 ( 61) hydrogen bonds : angle 6.90311 ( 141) SS BOND : bond 0.00234 ( 5) SS BOND : angle 1.31556 ( 10) covalent geometry : bond 0.00340 ( 3214) covalent geometry : angle 0.73177 ( 4377) *********************** 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 54 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.304 Fit side-chains REVERT: A 516 GLU cc_start: 0.8237 (pt0) cc_final: 0.8037 (pt0) REVERT: C 36 TYR cc_start: 0.7381 (m-80) cc_final: 0.6735 (m-80) outliers start: 6 outliers final: 6 residues processed: 52 average time/residue: 0.1558 time to fit residues: 9.9018 Evaluate side-chains 49 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 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 17 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.148555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.135981 restraints weight = 4668.379| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 1.62 r_work: 0.3685 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3220 Z= 0.183 Angle : 0.746 8.764 4390 Z= 0.378 Chirality : 0.049 0.195 479 Planarity : 0.007 0.111 561 Dihedral : 6.794 42.139 463 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.03 % Favored : 83.97 % Rotamer: Outliers : 2.37 % Allowed : 14.20 % 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 (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: -3.70 (0.41), residues: 393 helix: -4.96 (0.37), residues: 26 sheet: -1.97 (0.44), residues: 131 loop : -2.51 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 436 HIS 0.001 0.000 HIS A 519 PHE 0.036 0.002 PHE C 71 TYR 0.014 0.002 TYR C 49 ARG 0.011 0.001 ARG B 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00106 ( 1) link_NAG-ASN : angle 1.65792 ( 3) hydrogen bonds : bond 0.03685 ( 61) hydrogen bonds : angle 6.56895 ( 141) SS BOND : bond 0.00288 ( 5) SS BOND : angle 1.19387 ( 10) covalent geometry : bond 0.00429 ( 3214) covalent geometry : angle 0.74337 ( 4377) *********************** 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: 8 poor density : 52 time to evaluate : 0.339 Fit side-chains REVERT: A 457 ARG cc_start: 0.8702 (ttt-90) cc_final: 0.8246 (ttt-90) REVERT: B 47 TRP cc_start: 0.6267 (OUTLIER) cc_final: 0.5661 (t60) REVERT: C 36 TYR cc_start: 0.7572 (m-80) cc_final: 0.6538 (m-80) outliers start: 8 outliers final: 5 residues processed: 56 average time/residue: 0.1680 time to fit residues: 11.3036 Evaluate side-chains 53 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 83 ASN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 53 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 2.9990 chunk 7 optimal weight: 0.0570 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 0.0570 chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.5616 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.141661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.128260 restraints weight = 4759.768| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.90 r_work: 0.3553 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3220 Z= 0.146 Angle : 0.719 10.086 4390 Z= 0.363 Chirality : 0.047 0.187 479 Planarity : 0.007 0.101 561 Dihedral : 6.519 41.212 463 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.52 % Favored : 84.48 % Rotamer: Outliers : 2.96 % Allowed : 16.27 % 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 (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: -3.57 (0.41), residues: 393 helix: -4.96 (0.37), residues: 26 sheet: -1.73 (0.45), residues: 126 loop : -2.51 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 436 HIS 0.000 0.000 HIS A 519 PHE 0.032 0.002 PHE C 71 TYR 0.013 0.001 TYR C 49 ARG 0.008 0.001 ARG B 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00224 ( 1) link_NAG-ASN : angle 1.35948 ( 3) hydrogen bonds : bond 0.03296 ( 61) hydrogen bonds : angle 6.54237 ( 141) SS BOND : bond 0.00327 ( 5) SS BOND : angle 0.97881 ( 10) covalent geometry : bond 0.00347 ( 3214) covalent geometry : angle 0.71721 ( 4377) *********************** 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: 10 poor density : 50 time to evaluate : 0.308 Fit side-chains REVERT: A 457 ARG cc_start: 0.8716 (ttt-90) cc_final: 0.8146 (ttt-90) REVERT: B 47 TRP cc_start: 0.6085 (OUTLIER) cc_final: 0.5527 (t60) REVERT: C 36 TYR cc_start: 0.7532 (m-80) cc_final: 0.6530 (m-80) outliers start: 10 outliers final: 7 residues processed: 56 average time/residue: 0.1966 time to fit residues: 13.0103 Evaluate side-chains 54 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 THR 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 C residue 53 ASN 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 29 optimal weight: 3.9990 chunk 30 optimal weight: 0.0470 chunk 36 optimal weight: 0.6980 chunk 11 optimal weight: 0.0870 chunk 7 optimal weight: 0.0170 chunk 21 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 16 optimal weight: 0.0980 chunk 0 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 overall best weight: 0.1894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.146321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.132606 restraints weight = 4722.162| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 1.96 r_work: 0.3612 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3220 Z= 0.114 Angle : 0.677 11.008 4390 Z= 0.339 Chirality : 0.046 0.173 479 Planarity : 0.006 0.079 561 Dihedral : 5.989 37.680 463 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.74 % Favored : 86.26 % Rotamer: Outliers : 4.14 % Allowed : 18.64 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -3.41 (0.41), residues: 393 helix: -4.81 (0.45), residues: 26 sheet: -1.55 (0.46), residues: 126 loop : -2.46 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.000 0.000 HIS A 519 PHE 0.025 0.001 PHE C 71 TYR 0.014 0.001 TYR B 59 ARG 0.006 0.000 ARG B 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00255 ( 1) link_NAG-ASN : angle 1.14689 ( 3) hydrogen bonds : bond 0.02930 ( 61) hydrogen bonds : angle 6.51498 ( 141) SS BOND : bond 0.00153 ( 5) SS BOND : angle 1.15400 ( 10) covalent geometry : bond 0.00273 ( 3214) covalent geometry : angle 0.67465 ( 4377) *********************** 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 66 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.290 Fit side-chains REVERT: A 362 VAL cc_start: 0.8672 (OUTLIER) cc_final: 0.8414 (m) REVERT: A 457 ARG cc_start: 0.8671 (ttt-90) cc_final: 0.8270 (ttt-90) REVERT: A 516 GLU cc_start: 0.8325 (pt0) cc_final: 0.8032 (pt0) REVERT: B 39 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7795 (tt0) REVERT: C 5 THR cc_start: 0.8307 (m) cc_final: 0.7801 (p) REVERT: C 36 TYR cc_start: 0.7381 (m-80) cc_final: 0.6451 (m-80) outliers start: 14 outliers final: 8 residues processed: 61 average time/residue: 0.1801 time to fit residues: 12.9762 Evaluate side-chains 53 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL 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 104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 38 optimal weight: 0.0970 chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 21 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.3965 r_free = 0.3965 target = 0.152908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.139894 restraints weight = 4761.328| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 1.70 r_work: 0.3722 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3220 Z= 0.140 Angle : 0.697 11.060 4390 Z= 0.347 Chirality : 0.047 0.192 479 Planarity : 0.006 0.085 561 Dihedral : 6.075 37.234 463 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.25 % Favored : 85.75 % Rotamer: Outliers : 3.25 % Allowed : 19.82 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -3.25 (0.41), residues: 393 helix: -4.65 (0.59), residues: 20 sheet: -1.45 (0.46), residues: 126 loop : -2.43 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 112 HIS 0.001 0.001 HIS A 519 PHE 0.032 0.002 PHE C 71 TYR 0.012 0.001 TYR C 49 ARG 0.006 0.000 ARG B 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00178 ( 1) link_NAG-ASN : angle 1.49317 ( 3) hydrogen bonds : bond 0.03129 ( 61) hydrogen bonds : angle 6.31118 ( 141) SS BOND : bond 0.00216 ( 5) SS BOND : angle 1.28622 ( 10) covalent geometry : bond 0.00336 ( 3214) covalent geometry : angle 0.69386 ( 4377) *********************** 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 57 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.349 Fit side-chains REVERT: A 457 ARG cc_start: 0.8584 (ttt-90) cc_final: 0.8367 (ttt-90) REVERT: C 5 THR cc_start: 0.8340 (m) cc_final: 0.7894 (p) REVERT: C 36 TYR cc_start: 0.7452 (m-80) cc_final: 0.6501 (m-80) outliers start: 11 outliers final: 8 residues processed: 54 average time/residue: 0.1766 time to fit residues: 11.4954 Evaluate side-chains 50 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain B residue 19 SER 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 0.7980 chunk 17 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.143239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.129970 restraints weight = 4767.691| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.87 r_work: 0.3574 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 3220 Z= 0.159 Angle : 0.742 11.463 4390 Z= 0.371 Chirality : 0.049 0.206 479 Planarity : 0.006 0.081 561 Dihedral : 6.174 37.330 463 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.78 % Favored : 84.22 % Rotamer: Outliers : 3.85 % Allowed : 19.82 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -3.26 (0.41), residues: 393 helix: -4.72 (0.53), residues: 20 sheet: -1.43 (0.46), residues: 126 loop : -2.45 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.001 0.000 HIS A 519 PHE 0.036 0.002 PHE C 71 TYR 0.013 0.001 TYR C 49 ARG 0.005 0.000 ARG B 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00175 ( 1) link_NAG-ASN : angle 1.50636 ( 3) hydrogen bonds : bond 0.03271 ( 61) hydrogen bonds : angle 6.35263 ( 141) SS BOND : bond 0.00498 ( 5) SS BOND : angle 2.22331 ( 10) covalent geometry : bond 0.00384 ( 3214) covalent geometry : angle 0.73420 ( 4377) *********************** 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 56 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.351 Fit side-chains REVERT: A 457 ARG cc_start: 0.8656 (ttt-90) cc_final: 0.8221 (ttt-90) REVERT: A 516 GLU cc_start: 0.8283 (pt0) cc_final: 0.8012 (pt0) REVERT: C 5 THR cc_start: 0.8295 (m) cc_final: 0.7772 (p) REVERT: C 36 TYR cc_start: 0.7472 (m-80) cc_final: 0.6500 (m-80) outliers start: 13 outliers final: 10 residues processed: 53 average time/residue: 0.1633 time to fit residues: 10.5284 Evaluate side-chains 51 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ASN 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 51 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 73 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 15 optimal weight: 0.0870 chunk 30 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 1 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 = 0.3953 r_free = 0.3953 target = 0.152093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.139309 restraints weight = 4766.539| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 1.69 r_work: 0.3710 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3596 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 3220 Z= 0.156 Angle : 0.749 11.757 4390 Z= 0.374 Chirality : 0.049 0.193 479 Planarity : 0.006 0.082 561 Dihedral : 6.260 37.284 463 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.78 % Favored : 84.22 % Rotamer: Outliers : 3.25 % Allowed : 21.30 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -3.24 (0.41), residues: 393 helix: -4.72 (0.54), residues: 20 sheet: -1.46 (0.45), residues: 126 loop : -2.40 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.000 0.000 HIS A 519 PHE 0.034 0.002 PHE C 71 TYR 0.012 0.001 TYR C 49 ARG 0.005 0.000 ARG B 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00176 ( 1) link_NAG-ASN : angle 1.47939 ( 3) hydrogen bonds : bond 0.03348 ( 61) hydrogen bonds : angle 6.35913 ( 141) SS BOND : bond 0.00883 ( 5) SS BOND : angle 2.23371 ( 10) covalent geometry : bond 0.00377 ( 3214) covalent geometry : angle 0.74147 ( 4377) *********************** 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 57 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.410 Fit side-chains REVERT: A 457 ARG cc_start: 0.8623 (ttt-90) cc_final: 0.8142 (ttt-90) REVERT: A 516 GLU cc_start: 0.8124 (pt0) cc_final: 0.7908 (pt0) REVERT: C 5 THR cc_start: 0.8282 (m) cc_final: 0.7769 (p) REVERT: C 36 TYR cc_start: 0.7530 (m-80) cc_final: 0.6603 (m-80) outliers start: 11 outliers final: 9 residues processed: 54 average time/residue: 0.2269 time to fit residues: 14.9510 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 : 0.303 ------------------------------------------------------------------------------- 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 20 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 73 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 2 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 24 optimal weight: 0.0010 chunk 21 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 = 0.153112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.139739 restraints weight = 4754.943| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 1.79 r_work: 0.3705 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 3220 Z= 0.149 Angle : 0.736 12.169 4390 Z= 0.369 Chirality : 0.049 0.188 479 Planarity : 0.006 0.076 561 Dihedral : 6.258 37.692 463 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.27 % Favored : 84.73 % Rotamer: Outliers : 3.25 % Allowed : 22.49 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -3.18 (0.41), residues: 393 helix: -4.68 (0.56), residues: 20 sheet: -1.46 (0.45), residues: 126 loop : -2.34 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.000 0.000 HIS A 519 PHE 0.035 0.002 PHE C 71 TYR 0.013 0.001 TYR C 49 ARG 0.005 0.000 ARG B 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00181 ( 1) link_NAG-ASN : angle 1.46310 ( 3) hydrogen bonds : bond 0.03493 ( 61) hydrogen bonds : angle 6.28082 ( 141) SS BOND : bond 0.00686 ( 5) SS BOND : angle 2.12019 ( 10) covalent geometry : bond 0.00358 ( 3214) covalent geometry : angle 0.72948 ( 4377) *********************** 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 55 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.328 Fit side-chains REVERT: A 457 ARG cc_start: 0.8632 (ttt-90) cc_final: 0.8149 (ttt-90) REVERT: A 516 GLU cc_start: 0.8189 (pt0) cc_final: 0.7964 (pt0) REVERT: C 5 THR cc_start: 0.8275 (m) cc_final: 0.7760 (p) REVERT: C 36 TYR cc_start: 0.7532 (m-80) cc_final: 0.6590 (m-80) outliers start: 11 outliers final: 10 residues processed: 52 average time/residue: 0.1609 time to fit residues: 10.2624 Evaluate side-chains 53 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 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 51 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 8 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 chunk 24 optimal weight: 0.0770 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 3 optimal weight: 0.3980 chunk 4 optimal weight: 0.0870 chunk 18 optimal weight: 0.0980 chunk 34 optimal weight: 0.0670 chunk 9 optimal weight: 0.9990 overall best weight: 0.1454 ------------------------------------------------------------------------------- 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 = 0.4032 r_free = 0.4032 target = 0.159605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.146749 restraints weight = 4669.451| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 1.69 r_work: 0.3794 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3682 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2695 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= 0.115 Angle : 0.690 12.619 4390 Z= 0.344 Chirality : 0.047 0.171 479 Planarity : 0.005 0.051 561 Dihedral : 5.816 34.164 463 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.98 % Favored : 87.02 % Rotamer: Outliers : 1.48 % Allowed : 24.56 % 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 (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: -3.00 (0.41), residues: 393 helix: -4.82 (0.46), residues: 26 sheet: -1.21 (0.47), residues: 125 loop : -2.17 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 436 HIS 0.001 0.000 HIS A 519 PHE 0.025 0.001 PHE C 71 TYR 0.011 0.001 TYR C 49 ARG 0.004 0.000 ARG B 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00236 ( 1) link_NAG-ASN : angle 1.06487 ( 3) hydrogen bonds : bond 0.03155 ( 61) hydrogen bonds : angle 6.26071 ( 141) SS BOND : bond 0.00459 ( 5) SS BOND : angle 1.52428 ( 10) covalent geometry : bond 0.00277 ( 3214) covalent geometry : angle 0.68645 ( 4377) ********************** 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 48 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.367 Fit side-chains REVERT: A 444 LYS cc_start: 0.7324 (mmtt) cc_final: 0.7028 (mtpp) REVERT: A 467 ASP cc_start: 0.8477 (t0) cc_final: 0.8179 (t0) REVERT: A 516 GLU cc_start: 0.7987 (pt0) cc_final: 0.7751 (pt0) REVERT: C 5 THR cc_start: 0.8195 (m) cc_final: 0.7895 (p) REVERT: C 36 TYR cc_start: 0.7357 (m-80) cc_final: 0.6395 (m-80) outliers start: 5 outliers final: 5 residues processed: 47 average time/residue: 0.1730 time to fit residues: 9.9626 Evaluate side-chains 46 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 90 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 0.3980 chunk 17 optimal weight: 0.0470 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 14 optimal weight: 0.0050 chunk 34 optimal weight: 0.0370 chunk 8 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 overall best weight: 0.2570 ------------------------------------------------------------------------------- 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 = 0.4022 r_free = 0.4022 target = 0.158865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.145597 restraints weight = 4747.074| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 1.74 r_work: 0.3778 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3666 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3220 Z= 0.116 Angle : 0.685 11.991 4390 Z= 0.341 Chirality : 0.046 0.183 479 Planarity : 0.006 0.061 561 Dihedral : 5.773 33.404 463 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.47 % Favored : 87.53 % Rotamer: Outliers : 1.78 % Allowed : 25.44 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -2.87 (0.42), residues: 393 helix: -4.82 (0.45), residues: 26 sheet: -1.02 (0.50), residues: 115 loop : -2.10 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 36 HIS 0.000 0.000 HIS A 519 PHE 0.028 0.001 PHE C 71 TYR 0.012 0.001 TYR C 49 ARG 0.003 0.000 ARG B 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00191 ( 1) link_NAG-ASN : angle 1.37671 ( 3) hydrogen bonds : bond 0.03278 ( 61) hydrogen bonds : angle 6.10466 ( 141) SS BOND : bond 0.00533 ( 5) SS BOND : angle 1.59324 ( 10) covalent geometry : bond 0.00282 ( 3214) covalent geometry : angle 0.68131 ( 4377) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2349.09 seconds wall clock time: 41 minutes 21.95 seconds (2481.95 seconds total)