Starting phenix.real_space_refine on Wed Jun 4 16:23:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wm0_32596/06_2025/7wm0_32596.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wm0_32596/06_2025/7wm0_32596.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wm0_32596/06_2025/7wm0_32596.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wm0_32596/06_2025/7wm0_32596.map" model { file = "/net/cci-nas-00/data/ceres_data/7wm0_32596/06_2025/7wm0_32596.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wm0_32596/06_2025/7wm0_32596.cif" } resolution = 3.35 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= 0.005 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 17 5.16 5 C 2146 2.51 5 N 573 2.21 5 O 640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 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: 3376 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1554 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 182} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain breaks: 1 Chain: "L" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 841 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" 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: 3.68, per 1000 atoms: 1.09 Number of scatterers: 3376 At special positions: 0 Unit cell: (71.994, 79.092, 70.98, 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 17 16.00 O 640 8.00 N 573 7.00 C 2146 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.01 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.04 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 B1301 " - " ASN B 343 " Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 410.6 milliseconds 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 786 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 9 sheets defined 10.4% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.113A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.814A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.373A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.978A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.373A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.978A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.805A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.664A pdb=" N THR H 124 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR H 94 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL H 126 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.561A pdb=" N LEU L 11 " --> pdb=" O LYS L 108 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP L 110 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) 102 hydrogen bonds defined for protein. 243 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: 0.89 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1016 1.34 - 1.46: 795 1.46 - 1.59: 1630 1.59 - 1.71: 0 1.71 - 1.83: 22 Bond restraints: 3463 Sorted by residual: bond pdb=" N ILE B 472 " pdb=" CA ILE B 472 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.25e-02 6.40e+03 1.23e+01 bond pdb=" N VAL L 88 " pdb=" CA VAL L 88 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.14e-02 7.69e+03 1.18e+01 bond pdb=" N LYS B 444 " pdb=" CA LYS B 444 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.23e-02 6.61e+03 1.01e+01 bond pdb=" N ILE B 402 " pdb=" CA ILE B 402 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.01e+01 bond pdb=" N ASN H 54 " pdb=" CA ASN H 54 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.10e-02 8.26e+03 9.66e+00 ... (remaining 3458 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 3960 1.62 - 3.23: 630 3.23 - 4.85: 96 4.85 - 6.47: 15 6.47 - 8.09: 6 Bond angle restraints: 4707 Sorted by residual: angle pdb=" N SER B 366 " pdb=" CA SER B 366 " pdb=" C SER B 366 " ideal model delta sigma weight residual 111.71 105.91 5.80 1.15e+00 7.56e-01 2.54e+01 angle pdb=" N CYS B 432 " pdb=" CA CYS B 432 " pdb=" C CYS B 432 " ideal model delta sigma weight residual 109.85 116.70 -6.85 1.58e+00 4.01e-01 1.88e+01 angle pdb=" N ILE B 468 " pdb=" CA ILE B 468 " pdb=" C ILE B 468 " ideal model delta sigma weight residual 112.90 108.75 4.15 9.60e-01 1.09e+00 1.87e+01 angle pdb=" C VAL B 407 " pdb=" N ARG B 408 " pdb=" CA ARG B 408 " ideal model delta sigma weight residual 120.38 126.29 -5.91 1.37e+00 5.33e-01 1.86e+01 angle pdb=" N TYR B 369 " pdb=" CA TYR B 369 " pdb=" C TYR B 369 " ideal model delta sigma weight residual 112.89 108.02 4.87 1.24e+00 6.50e-01 1.54e+01 ... (remaining 4702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.97: 1807 13.97 - 27.95: 173 27.95 - 41.92: 53 41.92 - 55.90: 11 55.90 - 69.87: 7 Dihedral angle restraints: 2051 sinusoidal: 810 harmonic: 1241 Sorted by residual: dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 126.08 -33.08 1 1.00e+01 1.00e-02 1.56e+01 dihedral pdb=" C ARG B 466 " pdb=" N ARG B 466 " pdb=" CA ARG B 466 " pdb=" CB ARG B 466 " ideal model delta harmonic sigma weight residual -122.60 -114.01 -8.59 0 2.50e+00 1.60e-01 1.18e+01 dihedral pdb=" C TYR B 365 " pdb=" N TYR B 365 " pdb=" CA TYR B 365 " pdb=" CB TYR B 365 " ideal model delta harmonic sigma weight residual -122.60 -114.17 -8.43 0 2.50e+00 1.60e-01 1.14e+01 ... (remaining 2048 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 340 0.067 - 0.133: 117 0.133 - 0.200: 39 0.200 - 0.267: 8 0.267 - 0.333: 2 Chirality restraints: 506 Sorted by residual: chirality pdb=" CA ILE L 2 " pdb=" N ILE L 2 " pdb=" C ILE L 2 " pdb=" CB ILE L 2 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CA ARG B 466 " pdb=" N ARG B 466 " pdb=" C ARG B 466 " pdb=" CB ARG B 466 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA TYR H 115 " pdb=" N TYR H 115 " pdb=" C TYR H 115 " pdb=" CB TYR H 115 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 503 not shown) Planarity restraints: 612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1301 " -0.355 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C7 NAG B1301 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG B1301 " -0.137 2.00e-02 2.50e+03 pdb=" N2 NAG B1301 " 0.542 2.00e-02 2.50e+03 pdb=" O7 NAG B1301 " -0.133 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 353 " 0.013 2.00e-02 2.50e+03 2.70e-02 7.31e+00 pdb=" C TRP B 353 " -0.047 2.00e-02 2.50e+03 pdb=" O TRP B 353 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN B 354 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY H 116 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" C GLY H 116 " 0.037 2.00e-02 2.50e+03 pdb=" O GLY H 116 " -0.014 2.00e-02 2.50e+03 pdb=" N MET H 117 " -0.013 2.00e-02 2.50e+03 ... (remaining 609 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.90: 1446 2.90 - 3.40: 3021 3.40 - 3.90: 5401 3.90 - 4.40: 6057 4.40 - 4.90: 10403 Nonbonded interactions: 26328 Sorted by model distance: nonbonded pdb=" OD1 ASP H 62 " pdb=" N SER H 63 " model vdw 2.405 3.120 nonbonded pdb=" OD1 ASP H 118 " pdb=" N VAL H 119 " model vdw 2.423 3.120 nonbonded pdb=" NH1 ARG L 59 " pdb=" O PHE L 67 " model vdw 2.452 3.120 nonbonded pdb=" O SER H 130 " pdb=" OG SER H 130 " model vdw 2.456 3.040 nonbonded pdb=" NE2 GLN L 95 " pdb=" O PRO L 100 " model vdw 2.457 3.120 ... (remaining 26323 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: 2.510 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.190 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:2.910 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: 0.5482 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 : 0.009 0.044 3470 Z= 0.653 Angle : 1.227 8.086 4722 Z= 0.851 Chirality : 0.078 0.333 506 Planarity : 0.013 0.304 611 Dihedral : 12.602 69.871 1247 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.28 % Allowed : 6.89 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -2.87 (0.38), residues: 424 helix: -4.69 (0.22), residues: 39 sheet: -1.16 (0.45), residues: 142 loop : -1.89 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 353 HIS 0.005 0.001 HIS H 35 PHE 0.012 0.002 PHE B 515 TYR 0.012 0.002 TYR B 396 ARG 0.003 0.000 ARG B 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00929 ( 1) link_NAG-ASN : angle 1.90602 ( 3) hydrogen bonds : bond 0.20976 ( 102) hydrogen bonds : angle 9.12852 ( 243) SS BOND : bond 0.00851 ( 6) SS BOND : angle 2.24132 ( 12) covalent geometry : bond 0.00911 ( 3463) covalent geometry : angle 1.22259 ( 4707) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 30 ASP cc_start: 0.8174 (m-30) cc_final: 0.7972 (m-30) outliers start: 1 outliers final: 0 residues processed: 85 average time/residue: 0.1556 time to fit residues: 16.0432 Evaluate side-chains 55 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 0.0060 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 11 optimal weight: 0.0570 overall best weight: 0.4114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN H 13 GLN H 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.169825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.153385 restraints weight = 7628.599| |-----------------------------------------------------------------------------| r_work (start): 0.4330 rms_B_bonded: 4.28 r_work: 0.4190 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6310 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 3470 Z= 0.187 Angle : 0.687 7.693 4722 Z= 0.354 Chirality : 0.046 0.163 506 Planarity : 0.005 0.034 611 Dihedral : 6.043 52.043 499 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.20 % Allowed : 11.57 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.81 (0.39), residues: 424 helix: -4.66 (0.42), residues: 20 sheet: -0.64 (0.47), residues: 131 loop : -1.23 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 436 HIS 0.007 0.002 HIS H 35 PHE 0.025 0.002 PHE B 464 TYR 0.013 0.002 TYR B 421 ARG 0.005 0.001 ARG L 59 Details of bonding type rmsd link_NAG-ASN : bond 0.01225 ( 1) link_NAG-ASN : angle 3.73929 ( 3) hydrogen bonds : bond 0.04159 ( 102) hydrogen bonds : angle 6.79369 ( 243) SS BOND : bond 0.01104 ( 6) SS BOND : angle 1.52541 ( 12) covalent geometry : bond 0.00420 ( 3463) covalent geometry : angle 0.67763 ( 4707) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: B 380 TYR cc_start: 0.6372 (m-80) cc_final: 0.6172 (m-10) REVERT: H 90 ASP cc_start: 0.7455 (t70) cc_final: 0.7212 (t0) REVERT: H 102 MET cc_start: 0.7394 (mtm) cc_final: 0.6829 (mtm) outliers start: 8 outliers final: 7 residues processed: 70 average time/residue: 0.1266 time to fit residues: 11.4005 Evaluate side-chains 60 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 39 optimal weight: 0.0570 chunk 14 optimal weight: 0.5980 chunk 15 optimal weight: 0.0270 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 0.0980 chunk 1 optimal weight: 0.3980 overall best weight: 0.2356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN H 74 ASN L 31 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.169470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.155050 restraints weight = 7530.126| |-----------------------------------------------------------------------------| r_work (start): 0.4346 rms_B_bonded: 4.09 r_work: 0.4188 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6344 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3470 Z= 0.119 Angle : 0.591 6.991 4722 Z= 0.300 Chirality : 0.043 0.148 506 Planarity : 0.004 0.031 611 Dihedral : 5.745 54.453 499 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.48 % Allowed : 15.15 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.51 (0.40), residues: 424 helix: -4.45 (0.64), residues: 20 sheet: -0.34 (0.46), residues: 137 loop : -1.08 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 436 HIS 0.005 0.002 HIS H 35 PHE 0.010 0.001 PHE B 464 TYR 0.013 0.001 TYR B 508 ARG 0.003 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00196 ( 1) link_NAG-ASN : angle 3.12946 ( 3) hydrogen bonds : bond 0.03702 ( 102) hydrogen bonds : angle 6.21589 ( 243) SS BOND : bond 0.00440 ( 6) SS BOND : angle 0.77703 ( 12) covalent geometry : bond 0.00263 ( 3463) covalent geometry : angle 0.58518 ( 4707) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 380 TYR cc_start: 0.6363 (m-80) cc_final: 0.6144 (m-10) REVERT: H 90 ASP cc_start: 0.7324 (t70) cc_final: 0.7098 (t0) REVERT: H 102 MET cc_start: 0.7070 (mtm) cc_final: 0.6790 (mtm) outliers start: 9 outliers final: 6 residues processed: 72 average time/residue: 0.1381 time to fit residues: 12.5947 Evaluate side-chains 59 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 43 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 11 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.168136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.155203 restraints weight = 7570.179| |-----------------------------------------------------------------------------| r_work (start): 0.4422 rms_B_bonded: 3.66 r_work: 0.4276 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 moved from start: 0.5342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3470 Z= 0.186 Angle : 0.688 8.378 4722 Z= 0.358 Chirality : 0.045 0.149 506 Planarity : 0.005 0.034 611 Dihedral : 6.630 55.847 499 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 6.34 % Allowed : 16.80 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.28 (0.40), residues: 424 helix: -4.78 (0.41), residues: 26 sheet: 0.15 (0.47), residues: 130 loop : -0.96 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 436 HIS 0.005 0.002 HIS H 35 PHE 0.010 0.002 PHE B 377 TYR 0.045 0.003 TYR B 508 ARG 0.005 0.001 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00058 ( 1) link_NAG-ASN : angle 3.72121 ( 3) hydrogen bonds : bond 0.03977 ( 102) hydrogen bonds : angle 6.40225 ( 243) SS BOND : bond 0.00488 ( 6) SS BOND : angle 1.21125 ( 12) covalent geometry : bond 0.00421 ( 3463) covalent geometry : angle 0.67982 ( 4707) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.354 Fit side-chains REVERT: B 378 LYS cc_start: 0.7446 (mtmt) cc_final: 0.7182 (mmtm) REVERT: B 380 TYR cc_start: 0.6367 (m-80) cc_final: 0.6155 (m-80) REVERT: B 449 TYR cc_start: 0.6675 (t80) cc_final: 0.6394 (t80) REVERT: B 501 TYR cc_start: 0.4453 (OUTLIER) cc_final: 0.4075 (m-10) REVERT: H 90 ASP cc_start: 0.7402 (t70) cc_final: 0.7143 (t0) REVERT: H 102 MET cc_start: 0.7111 (mtm) cc_final: 0.6596 (mtm) REVERT: L 31 HIS cc_start: 0.5590 (OUTLIER) cc_final: 0.5255 (t70) outliers start: 23 outliers final: 15 residues processed: 80 average time/residue: 0.1367 time to fit residues: 13.7680 Evaluate side-chains 73 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 31 HIS Chi-restraints excluded: chain L residue 99 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 0.0870 chunk 25 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.159839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.145307 restraints weight = 7520.624| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 4.14 r_work: 0.4065 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.6055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3470 Z= 0.173 Angle : 0.677 7.671 4722 Z= 0.346 Chirality : 0.044 0.148 506 Planarity : 0.005 0.033 611 Dihedral : 6.443 49.695 499 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 6.06 % Allowed : 17.63 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.36 (0.40), residues: 424 helix: -4.81 (0.38), residues: 26 sheet: 0.17 (0.48), residues: 131 loop : -1.07 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 436 HIS 0.005 0.001 HIS H 35 PHE 0.013 0.002 PHE H 29 TYR 0.040 0.002 TYR B 508 ARG 0.004 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00105 ( 1) link_NAG-ASN : angle 3.67206 ( 3) hydrogen bonds : bond 0.03715 ( 102) hydrogen bonds : angle 6.31812 ( 243) SS BOND : bond 0.00464 ( 6) SS BOND : angle 1.08030 ( 12) covalent geometry : bond 0.00391 ( 3463) covalent geometry : angle 0.66960 ( 4707) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: B 378 LYS cc_start: 0.7552 (mtmt) cc_final: 0.7245 (mmtm) REVERT: B 380 TYR cc_start: 0.6642 (m-80) cc_final: 0.6357 (m-80) REVERT: B 449 TYR cc_start: 0.6897 (t80) cc_final: 0.6468 (t80) REVERT: H 102 MET cc_start: 0.6863 (mtm) cc_final: 0.6575 (mtm) REVERT: L 31 HIS cc_start: 0.5757 (OUTLIER) cc_final: 0.5266 (t70) outliers start: 22 outliers final: 16 residues processed: 86 average time/residue: 0.1738 time to fit residues: 17.9005 Evaluate side-chains 74 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain L residue 31 HIS Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 55 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 20 optimal weight: 0.4980 chunk 0 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 13 GLN H 35 HIS H 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.163163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.150526 restraints weight = 7739.393| |-----------------------------------------------------------------------------| r_work (start): 0.4343 rms_B_bonded: 3.76 r_work: 0.4170 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.7111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 3470 Z= 0.239 Angle : 0.780 8.697 4722 Z= 0.403 Chirality : 0.047 0.151 506 Planarity : 0.005 0.042 611 Dihedral : 7.147 40.836 499 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 6.06 % Allowed : 21.21 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.57 (0.40), residues: 424 helix: -4.97 (0.27), residues: 26 sheet: 0.17 (0.50), residues: 125 loop : -1.28 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 436 HIS 0.004 0.002 HIS L 31 PHE 0.017 0.003 PHE B 374 TYR 0.022 0.003 TYR B 508 ARG 0.003 0.001 ARG B 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00159 ( 1) link_NAG-ASN : angle 4.21979 ( 3) hydrogen bonds : bond 0.04445 ( 102) hydrogen bonds : angle 6.75128 ( 243) SS BOND : bond 0.00423 ( 6) SS BOND : angle 1.16604 ( 12) covalent geometry : bond 0.00541 ( 3463) covalent geometry : angle 0.77212 ( 4707) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.378 Fit side-chains REVERT: B 378 LYS cc_start: 0.7611 (mtmt) cc_final: 0.7404 (mmtm) outliers start: 22 outliers final: 17 residues processed: 83 average time/residue: 0.1291 time to fit residues: 13.6909 Evaluate side-chains 73 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 14 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 74 ASN L 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.153599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.141515 restraints weight = 7411.511| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 3.76 r_work: 0.4005 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.7589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 3470 Z= 0.221 Angle : 0.776 10.759 4722 Z= 0.392 Chirality : 0.046 0.172 506 Planarity : 0.005 0.039 611 Dihedral : 7.003 35.923 499 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 6.06 % Allowed : 24.24 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.81 (0.39), residues: 424 helix: -5.02 (0.24), residues: 26 sheet: 0.08 (0.50), residues: 121 loop : -1.48 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 436 HIS 0.005 0.001 HIS B 505 PHE 0.036 0.002 PHE B 429 TYR 0.021 0.002 TYR B 508 ARG 0.003 0.001 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00111 ( 1) link_NAG-ASN : angle 4.10682 ( 3) hydrogen bonds : bond 0.03960 ( 102) hydrogen bonds : angle 6.64880 ( 243) SS BOND : bond 0.00382 ( 6) SS BOND : angle 1.16347 ( 12) covalent geometry : bond 0.00502 ( 3463) covalent geometry : angle 0.76758 ( 4707) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.360 Fit side-chains outliers start: 22 outliers final: 19 residues processed: 81 average time/residue: 0.1178 time to fit residues: 12.4000 Evaluate side-chains 77 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 20 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 21 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 74 ASN L 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.153567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.141364 restraints weight = 7456.052| |-----------------------------------------------------------------------------| r_work (start): 0.4170 rms_B_bonded: 3.93 r_work: 0.3998 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.7938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3470 Z= 0.202 Angle : 0.770 11.848 4722 Z= 0.386 Chirality : 0.046 0.169 506 Planarity : 0.005 0.040 611 Dihedral : 6.949 35.080 499 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 5.51 % Allowed : 24.79 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.97 (0.39), residues: 424 helix: -5.02 (0.23), residues: 26 sheet: -0.10 (0.49), residues: 128 loop : -1.60 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 436 HIS 0.004 0.001 HIS B 505 PHE 0.042 0.003 PHE B 429 TYR 0.027 0.002 TYR B 508 ARG 0.005 0.001 ARG B 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00124 ( 1) link_NAG-ASN : angle 4.06410 ( 3) hydrogen bonds : bond 0.03935 ( 102) hydrogen bonds : angle 6.56022 ( 243) SS BOND : bond 0.00456 ( 6) SS BOND : angle 1.18101 ( 12) covalent geometry : bond 0.00462 ( 3463) covalent geometry : angle 0.76223 ( 4707) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.367 Fit side-chains REVERT: B 449 TYR cc_start: 0.7079 (t80) cc_final: 0.6557 (t80) outliers start: 20 outliers final: 19 residues processed: 75 average time/residue: 0.1229 time to fit residues: 11.8350 Evaluate side-chains 74 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 31 HIS Chi-restraints excluded: chain L residue 55 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.2980 chunk 5 optimal weight: 0.5980 chunk 36 optimal weight: 0.0870 chunk 14 optimal weight: 0.0010 chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.0770 chunk 0 optimal weight: 0.1980 chunk 1 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN H 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.158866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.146761 restraints weight = 7451.079| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 3.89 r_work: 0.4067 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.7875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3470 Z= 0.124 Angle : 0.694 8.384 4722 Z= 0.348 Chirality : 0.044 0.147 506 Planarity : 0.004 0.032 611 Dihedral : 6.153 32.238 499 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.86 % Allowed : 26.17 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 (0.39), residues: 424 helix: -4.97 (0.25), residues: 26 sheet: 0.41 (0.54), residues: 112 loop : -1.48 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 36 HIS 0.006 0.001 HIS L 31 PHE 0.036 0.002 PHE B 429 TYR 0.015 0.001 TYR B 508 ARG 0.004 0.000 ARG B 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 1) link_NAG-ASN : angle 3.60886 ( 3) hydrogen bonds : bond 0.03028 ( 102) hydrogen bonds : angle 6.20087 ( 243) SS BOND : bond 0.00329 ( 6) SS BOND : angle 0.87674 ( 12) covalent geometry : bond 0.00282 ( 3463) covalent geometry : angle 0.68730 ( 4707) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.385 Fit side-chains REVERT: B 378 LYS cc_start: 0.7744 (mmtm) cc_final: 0.7172 (pttm) REVERT: B 449 TYR cc_start: 0.6691 (t80) cc_final: 0.6266 (t80) REVERT: H 90 ASP cc_start: 0.7497 (t70) cc_final: 0.7111 (t0) outliers start: 14 outliers final: 13 residues processed: 72 average time/residue: 0.1146 time to fit residues: 10.8542 Evaluate side-chains 70 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 55 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.0980 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 chunk 22 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 0.0970 chunk 23 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 0.0970 chunk 31 optimal weight: 0.5980 overall best weight: 0.2776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN H 74 ASN L 31 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.157914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.147557 restraints weight = 7254.575| |-----------------------------------------------------------------------------| r_work (start): 0.4248 rms_B_bonded: 3.21 r_work: 0.4116 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.7988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3470 Z= 0.137 Angle : 0.699 8.796 4722 Z= 0.351 Chirality : 0.044 0.148 506 Planarity : 0.004 0.035 611 Dihedral : 6.182 34.941 499 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.13 % Allowed : 26.72 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.61 (0.39), residues: 424 helix: -4.94 (0.25), residues: 26 sheet: 0.44 (0.53), residues: 112 loop : -1.40 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 436 HIS 0.002 0.001 HIS B 505 PHE 0.033 0.002 PHE B 429 TYR 0.016 0.002 TYR B 508 ARG 0.005 0.000 ARG B 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00115 ( 1) link_NAG-ASN : angle 3.71666 ( 3) hydrogen bonds : bond 0.03323 ( 102) hydrogen bonds : angle 6.10335 ( 243) SS BOND : bond 0.00284 ( 6) SS BOND : angle 1.64465 ( 12) covalent geometry : bond 0.00319 ( 3463) covalent geometry : angle 0.68844 ( 4707) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: B 449 TYR cc_start: 0.6480 (t80) cc_final: 0.6222 (t80) outliers start: 15 outliers final: 15 residues processed: 76 average time/residue: 0.1198 time to fit residues: 11.8644 Evaluate side-chains 75 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 31 HIS Chi-restraints excluded: chain L residue 55 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 12 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 0.0060 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 chunk 1 optimal weight: 0.6980 chunk 23 optimal weight: 0.3980 chunk 30 optimal weight: 0.9980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.154878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.142794 restraints weight = 7440.024| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 3.88 r_work: 0.4026 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.8196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3470 Z= 0.178 Angle : 0.756 8.998 4722 Z= 0.380 Chirality : 0.046 0.154 506 Planarity : 0.005 0.035 611 Dihedral : 6.499 38.324 499 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.86 % Allowed : 27.00 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.86 (0.39), residues: 424 helix: -4.95 (0.24), residues: 26 sheet: 0.19 (0.51), residues: 122 loop : -1.61 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 36 HIS 0.005 0.002 HIS L 31 PHE 0.033 0.002 PHE B 429 TYR 0.019 0.002 TYR B 508 ARG 0.002 0.000 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00021 ( 1) link_NAG-ASN : angle 3.89409 ( 3) hydrogen bonds : bond 0.03650 ( 102) hydrogen bonds : angle 6.23362 ( 243) SS BOND : bond 0.00374 ( 6) SS BOND : angle 1.88322 ( 12) covalent geometry : bond 0.00410 ( 3463) covalent geometry : angle 0.74504 ( 4707) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2369.90 seconds wall clock time: 41 minutes 17.16 seconds (2477.16 seconds total)