Starting phenix.real_space_refine on Wed Sep 17 03:50:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wm0_32596/09_2025/7wm0_32596.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wm0_32596/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7wm0_32596/09_2025/7wm0_32596.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wm0_32596/09_2025/7wm0_32596.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wm0_32596/09_2025/7wm0_32596.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wm0_32596/09_2025/7wm0_32596.map" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.14, per 1000 atoms: 0.34 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: 0.31 Conformation dependent library (CDL) restraints added in 144.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.16 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: 0.51 Time building geometry restraints manager: 0.41 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: 3.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.660 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.820 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.003 0.000 ARG B 454 TYR 0.012 0.002 TYR B 396 PHE 0.012 0.002 PHE B 515 TRP 0.008 0.002 TRP B 353 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00911 ( 3463) covalent geometry : angle 1.22259 ( 4707) SS BOND : bond 0.00851 ( 6) SS BOND : angle 2.24132 ( 12) hydrogen bonds : bond 0.20976 ( 102) hydrogen bonds : angle 9.12852 ( 243) link_NAG-ASN : bond 0.00929 ( 1) link_NAG-ASN : angle 1.90602 ( 3) *********************** 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 : 0.126 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: 0.0700 time to fit residues: 7.2927 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 : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.4980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.4483 r_free = 0.4483 target = 0.166452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.150695 restraints weight = 7688.759| |-----------------------------------------------------------------------------| r_work (start): 0.4296 rms_B_bonded: 4.24 r_work: 0.4140 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6440 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 3470 Z= 0.206 Angle : 0.746 8.270 4722 Z= 0.386 Chirality : 0.047 0.165 506 Planarity : 0.005 0.035 611 Dihedral : 6.588 54.944 499 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.20 % Allowed : 11.85 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.38), residues: 424 helix: -4.68 (0.37), residues: 20 sheet: -0.68 (0.45), residues: 136 loop : -1.32 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 59 TYR 0.016 0.002 TYR L 92 PHE 0.025 0.002 PHE B 464 TRP 0.014 0.002 TRP B 436 HIS 0.007 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 3463) covalent geometry : angle 0.73052 ( 4707) SS BOND : bond 0.00392 ( 6) SS BOND : angle 1.59420 ( 12) hydrogen bonds : bond 0.04026 ( 102) hydrogen bonds : angle 6.87635 ( 243) link_NAG-ASN : bond 0.00160 ( 1) link_NAG-ASN : angle 5.23304 ( 3) *********************** 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 76 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.103 Fit side-chains REVERT: B 378 LYS cc_start: 0.7508 (mtmt) cc_final: 0.6867 (mmtm) REVERT: H 102 MET cc_start: 0.7393 (mtm) cc_final: 0.6804 (mtm) outliers start: 8 outliers final: 7 residues processed: 73 average time/residue: 0.0597 time to fit residues: 5.4648 Evaluate side-chains 63 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.152 ------------------------------------------------------------------------------- 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 32 optimal weight: 0.1980 chunk 21 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4561 r_free = 0.4561 target = 0.167289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.154659 restraints weight = 7422.166| |-----------------------------------------------------------------------------| r_work (start): 0.4413 rms_B_bonded: 3.55 r_work: 0.4265 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.4265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6533 moved from start: 0.5354 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= 0.205 Angle : 0.725 8.139 4722 Z= 0.379 Chirality : 0.046 0.165 506 Planarity : 0.005 0.035 611 Dihedral : 6.818 56.355 499 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.68 % Allowed : 15.15 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (0.39), residues: 424 helix: -4.76 (0.44), residues: 26 sheet: -0.23 (0.48), residues: 121 loop : -1.12 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 457 TYR 0.020 0.002 TYR B 508 PHE 0.011 0.002 PHE B 464 TRP 0.025 0.002 TRP B 436 HIS 0.008 0.002 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 3463) covalent geometry : angle 0.71577 ( 4707) SS BOND : bond 0.00634 ( 6) SS BOND : angle 1.58859 ( 12) hydrogen bonds : bond 0.04484 ( 102) hydrogen bonds : angle 6.53897 ( 243) link_NAG-ASN : bond 0.00021 ( 1) link_NAG-ASN : angle 3.50820 ( 3) *********************** 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 78 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 378 LYS cc_start: 0.7383 (mtmt) cc_final: 0.7036 (mmtm) REVERT: B 405 ASP cc_start: 0.6138 (m-30) cc_final: 0.5885 (t0) REVERT: H 102 MET cc_start: 0.6949 (mtm) cc_final: 0.6677 (mtm) outliers start: 17 outliers final: 11 residues processed: 73 average time/residue: 0.0629 time to fit residues: 5.6971 Evaluate side-chains 63 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.089 ------------------------------------------------------------------------------- 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 517 LEU 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 99 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.2980 chunk 10 optimal weight: 0.7980 chunk 9 optimal weight: 0.0170 chunk 0 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 0.0980 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 0.0570 overall best weight: 0.1336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 74 ASN L 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.171735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.158991 restraints weight = 7448.446| |-----------------------------------------------------------------------------| r_work (start): 0.4444 rms_B_bonded: 3.60 r_work: 0.4304 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.4304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6436 moved from start: 0.5550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3470 Z= 0.110 Angle : 0.628 7.580 4722 Z= 0.318 Chirality : 0.042 0.147 506 Planarity : 0.004 0.030 611 Dihedral : 6.308 54.585 499 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.68 % Allowed : 16.80 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.40), residues: 424 helix: -4.71 (0.46), residues: 26 sheet: -0.03 (0.47), residues: 134 loop : -0.91 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 509 TYR 0.025 0.001 TYR B 508 PHE 0.008 0.001 PHE B 464 TRP 0.013 0.001 TRP B 436 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 3463) covalent geometry : angle 0.62096 ( 4707) SS BOND : bond 0.00450 ( 6) SS BOND : angle 1.01810 ( 12) hydrogen bonds : bond 0.03364 ( 102) hydrogen bonds : angle 6.19118 ( 243) link_NAG-ASN : bond 0.00257 ( 1) link_NAG-ASN : angle 3.33931 ( 3) *********************** 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 79 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.078 Fit side-chains REVERT: B 378 LYS cc_start: 0.7310 (mtmt) cc_final: 0.7106 (mmtm) REVERT: H 90 ASP cc_start: 0.7279 (t70) cc_final: 0.6963 (t0) REVERT: H 102 MET cc_start: 0.6908 (mtm) cc_final: 0.6690 (mtm) outliers start: 17 outliers final: 8 residues processed: 72 average time/residue: 0.0613 time to fit residues: 5.5071 Evaluate side-chains 70 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 383 SER 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 517 LEU Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 79 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 0.9980 chunk 37 optimal weight: 0.0870 chunk 26 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 38 optimal weight: 0.2980 chunk 20 optimal weight: 0.0170 overall best weight: 0.3796 ------------------------------------------------------------------------------- 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 ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.169319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.155452 restraints weight = 7462.370| |-----------------------------------------------------------------------------| r_work (start): 0.4405 rms_B_bonded: 3.79 r_work: 0.4262 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.6164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3470 Z= 0.151 Angle : 0.687 8.621 4722 Z= 0.346 Chirality : 0.044 0.145 506 Planarity : 0.004 0.029 611 Dihedral : 6.362 50.603 499 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.58 % Allowed : 19.01 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.40), residues: 424 helix: -4.78 (0.42), residues: 26 sheet: 0.17 (0.48), residues: 131 loop : -0.93 (0.37), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 457 TYR 0.014 0.002 TYR B 473 PHE 0.010 0.002 PHE B 374 TRP 0.023 0.002 TRP B 436 HIS 0.004 0.002 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 3463) covalent geometry : angle 0.67618 ( 4707) SS BOND : bond 0.00417 ( 6) SS BOND : angle 1.78583 ( 12) hydrogen bonds : bond 0.03659 ( 102) hydrogen bonds : angle 6.23891 ( 243) link_NAG-ASN : bond 0.00099 ( 1) link_NAG-ASN : angle 3.57328 ( 3) *********************** 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 82 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.129 Fit side-chains REVERT: B 449 TYR cc_start: 0.6734 (t80) cc_final: 0.6381 (t80) outliers start: 13 outliers final: 12 residues processed: 78 average time/residue: 0.0608 time to fit residues: 5.9581 Evaluate side-chains 71 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 383 SER 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 517 LEU Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 30 ASP 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 15 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 0.0970 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.0970 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.4176 ------------------------------------------------------------------------------- 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 ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.167341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.154853 restraints weight = 7454.155| |-----------------------------------------------------------------------------| r_work (start): 0.4390 rms_B_bonded: 3.52 r_work: 0.4225 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.6652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3470 Z= 0.160 Angle : 0.678 7.748 4722 Z= 0.345 Chirality : 0.043 0.150 506 Planarity : 0.004 0.031 611 Dihedral : 6.375 45.593 499 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.96 % Allowed : 22.87 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.40), residues: 424 helix: -4.88 (0.35), residues: 26 sheet: 0.24 (0.48), residues: 130 loop : -1.00 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 457 TYR 0.020 0.002 TYR B 508 PHE 0.007 0.002 PHE B 374 TRP 0.018 0.002 TRP B 436 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 3463) covalent geometry : angle 0.67094 ( 4707) SS BOND : bond 0.00392 ( 6) SS BOND : angle 1.07402 ( 12) hydrogen bonds : bond 0.03561 ( 102) hydrogen bonds : angle 6.23184 ( 243) link_NAG-ASN : bond 0.00074 ( 1) link_NAG-ASN : angle 3.67808 ( 3) *********************** 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 83 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.168 Fit side-chains REVERT: B 449 TYR cc_start: 0.6875 (t80) cc_final: 0.6418 (t80) outliers start: 18 outliers final: 16 residues processed: 80 average time/residue: 0.0559 time to fit residues: 5.7395 Evaluate side-chains 78 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.113 ------------------------------------------------------------------------------- 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 470 THR Chi-restraints excluded: chain B residue 477 ASN 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 30 ASP Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 55 SER 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 102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 14 optimal weight: 0.2980 chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 0.2980 chunk 17 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 13 GLN H 35 HIS H 74 ASN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.163528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.150383 restraints weight = 7560.437| |-----------------------------------------------------------------------------| r_work (start): 0.4343 rms_B_bonded: 3.72 r_work: 0.4172 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.7212 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= 0.214 Angle : 0.758 8.001 4722 Z= 0.386 Chirality : 0.045 0.163 506 Planarity : 0.005 0.034 611 Dihedral : 6.733 41.984 499 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 5.79 % Allowed : 22.59 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.40), residues: 424 helix: -4.94 (0.30), residues: 26 sheet: 0.12 (0.48), residues: 131 loop : -1.17 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 19 TYR 0.021 0.002 TYR B 508 PHE 0.009 0.002 PHE B 377 TRP 0.022 0.002 TRP B 436 HIS 0.004 0.001 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 3463) covalent geometry : angle 0.75074 ( 4707) SS BOND : bond 0.00507 ( 6) SS BOND : angle 0.95829 ( 12) hydrogen bonds : bond 0.03986 ( 102) hydrogen bonds : angle 6.49989 ( 243) link_NAG-ASN : bond 0.00121 ( 1) link_NAG-ASN : angle 3.98334 ( 3) *********************** 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 86 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.231 Fit side-chains outliers start: 21 outliers final: 20 residues processed: 82 average time/residue: 0.0672 time to fit residues: 6.7958 Evaluate side-chains 79 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.119 ------------------------------------------------------------------------------- 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 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 30 ASP Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 55 SER 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 13 VAL Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 90 VAL 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 30 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 41 optimal weight: 0.0970 chunk 9 optimal weight: 0.9980 chunk 26 optimal weight: 0.0970 chunk 12 optimal weight: 0.6980 chunk 4 optimal weight: 0.2980 overall best weight: 0.3176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 74 ASN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.165789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.153514 restraints weight = 7572.177| |-----------------------------------------------------------------------------| r_work (start): 0.4379 rms_B_bonded: 3.48 r_work: 0.4214 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.7393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3470 Z= 0.140 Angle : 0.695 8.693 4722 Z= 0.349 Chirality : 0.044 0.151 506 Planarity : 0.004 0.031 611 Dihedral : 6.339 39.216 499 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.68 % Allowed : 26.72 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.40), residues: 424 helix: -4.93 (0.29), residues: 26 sheet: 0.25 (0.49), residues: 129 loop : -1.13 (0.36), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 454 TYR 0.018 0.002 TYR B 380 PHE 0.018 0.002 PHE B 429 TRP 0.015 0.002 TRP B 436 HIS 0.003 0.001 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 3463) covalent geometry : angle 0.68810 ( 4707) SS BOND : bond 0.00425 ( 6) SS BOND : angle 0.85667 ( 12) hydrogen bonds : bond 0.03342 ( 102) hydrogen bonds : angle 6.25082 ( 243) link_NAG-ASN : bond 0.00090 ( 1) link_NAG-ASN : angle 3.65994 ( 3) *********************** 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 81 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.130 Fit side-chains REVERT: H 21 SER cc_start: 0.8161 (t) cc_final: 0.7959 (m) outliers start: 17 outliers final: 15 residues processed: 79 average time/residue: 0.0492 time to fit residues: 5.0730 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 : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 383 SER 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 30 ASP Chi-restraints excluded: chain H residue 55 SER 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 90 VAL Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 12 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.153725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.140769 restraints weight = 7367.806| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 3.91 r_work: 0.4002 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.7915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 3470 Z= 0.223 Angle : 0.783 8.888 4722 Z= 0.399 Chirality : 0.047 0.167 506 Planarity : 0.005 0.038 611 Dihedral : 6.928 41.313 499 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.13 % Allowed : 27.55 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.39), residues: 424 helix: -4.97 (0.25), residues: 26 sheet: 0.34 (0.51), residues: 117 loop : -1.41 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 454 TYR 0.023 0.002 TYR B 508 PHE 0.016 0.002 PHE B 374 TRP 0.024 0.002 TRP B 436 HIS 0.003 0.001 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00509 ( 3463) covalent geometry : angle 0.77511 ( 4707) SS BOND : bond 0.00516 ( 6) SS BOND : angle 1.16939 ( 12) hydrogen bonds : bond 0.03935 ( 102) hydrogen bonds : angle 6.66978 ( 243) link_NAG-ASN : bond 0.00172 ( 1) link_NAG-ASN : angle 4.10276 ( 3) *********************** 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 80 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.131 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 15 residues processed: 77 average time/residue: 0.0476 time to fit residues: 4.7488 Evaluate side-chains 77 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 383 SER 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 30 ASP Chi-restraints excluded: chain H residue 55 SER 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 83 MET Chi-restraints excluded: chain L residue 90 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 0.0870 chunk 36 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 20 optimal weight: 0.0170 chunk 32 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 27 optimal weight: 0.1980 chunk 8 optimal weight: 0.6980 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 506 GLN H 74 ASN H 82 HIS ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.156972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.144149 restraints weight = 7336.454| |-----------------------------------------------------------------------------| r_work (start): 0.4207 rms_B_bonded: 3.84 r_work: 0.4040 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.7978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3470 Z= 0.138 Angle : 0.696 6.866 4722 Z= 0.352 Chirality : 0.044 0.149 506 Planarity : 0.004 0.034 611 Dihedral : 6.316 37.790 499 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.58 % Allowed : 28.37 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.39), residues: 424 helix: -4.90 (0.26), residues: 26 sheet: 0.29 (0.51), residues: 119 loop : -1.36 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 454 TYR 0.017 0.002 TYR B 508 PHE 0.012 0.002 PHE B 429 TRP 0.013 0.002 TRP B 436 HIS 0.001 0.001 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 3463) covalent geometry : angle 0.68695 ( 4707) SS BOND : bond 0.00269 ( 6) SS BOND : angle 1.55094 ( 12) hydrogen bonds : bond 0.03240 ( 102) hydrogen bonds : angle 6.25994 ( 243) link_NAG-ASN : bond 0.00106 ( 1) link_NAG-ASN : angle 3.66257 ( 3) ********************** 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 70 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.134 Fit side-chains revert: symmetry clash REVERT: H 21 SER cc_start: 0.8164 (t) cc_final: 0.7923 (m) outliers start: 13 outliers final: 13 residues processed: 67 average time/residue: 0.0541 time to fit residues: 4.6912 Evaluate side-chains 67 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR 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 30 ASP Chi-restraints excluded: chain H residue 55 SER 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 83 MET Chi-restraints excluded: chain L residue 90 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 1 optimal weight: 0.2980 chunk 11 optimal weight: 0.0980 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 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 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.153864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.141065 restraints weight = 7469.755| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 3.84 r_work: 0.4009 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.8221 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= 0.188 Angle : 0.749 7.880 4722 Z= 0.380 Chirality : 0.046 0.159 506 Planarity : 0.005 0.035 611 Dihedral : 6.647 41.656 499 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 4.68 % Allowed : 26.45 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.39), residues: 424 helix: -4.93 (0.25), residues: 26 sheet: 0.48 (0.52), residues: 115 loop : -1.55 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 19 TYR 0.021 0.002 TYR B 508 PHE 0.013 0.002 PHE B 374 TRP 0.023 0.002 TRP B 436 HIS 0.004 0.001 HIS H 82 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 3463) covalent geometry : angle 0.73780 ( 4707) SS BOND : bond 0.00374 ( 6) SS BOND : angle 1.78248 ( 12) hydrogen bonds : bond 0.03796 ( 102) hydrogen bonds : angle 6.50416 ( 243) link_NAG-ASN : bond 0.00090 ( 1) link_NAG-ASN : angle 3.90410 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1198.69 seconds wall clock time: 21 minutes 20.61 seconds (1280.61 seconds total)